When Employer Deductions Are Legal Under Philippine Law
Wage protection is a central theme of Philippine labor law. As a rule, employees must receive their wages in full, on time, and without employer-imposed “charges” that shift business losses to labor. This is why the law tightly restricts payroll deductions and treats “variance” schemes (cash shortages, inventory discrepancies, breakage, etc.) with particular suspicion.
This article explains what Philippine law allows, what it prohibits, and how “variance” deductions can be lawful only in narrow, well-documented circumstances.
1) The governing principle: wages are protected and must generally be paid in full
Philippine labor policy (anchored in the Constitution’s protection to labor and the Labor Code’s wage provisions) treats wages as property meant to support workers and their families. The Labor Code therefore:
- restricts when wages may be deducted,
- limits “deposits” or “cash bonds,” and
- bans schemes that effectively force employees to pay the employer as a condition of employment.
In practice, any deduction that is not clearly authorized will be presumed illegal—especially when it resembles a penalty, a kickback, or a method to pass ordinary business risk to employees.
2) What counts as “wages” (and why it matters)
“Wages” generally include remuneration for work performed, including items treated as part of wage by law (e.g., properly deductible “facilities” under strict rules). This matters because the wage-protection rules apply not only to base pay but also commonly to:
- daily wages / salary,
- overtime pay, holiday pay, rest day premium,
- night shift differential,
- 13th month pay and other cash benefits (subject to their own rules but still protected from unauthorized withholding),
- final pay upon separation.
If the amount is part of compensation or a legally required premium, deductions from it must still have a lawful basis.
3) The core rule on salary deductions: no deduction unless the law clearly allows it
Under the Labor Code’s wage-protection provisions, an employer generally may not deduct from wages unless the deduction falls under a recognized legal category. A company policy, handbook, memo, or “standard practice” is not enough by itself.
Think of lawful deductions in three big buckets:
- Deductions required or authorized by law / lawful orders
- Deductions authorized by the employee (usually in writing) under strict conditions
- Deductions for proven employee responsibility for loss/damage, after due process, under narrow rules
“Variance” charges typically try to squeeze into bucket #3—but often fail.
4) Lawful deductions: the main categories
A) Statutory (legally required) deductions
These are the safest and most common lawful deductions, because they are expressly mandated by law or valid legal process, such as:
- Withholding tax on compensation (under tax law)
- SSS contributions (employee share withheld by employer; employer remits)
- PhilHealth contributions (employee share withheld by employer; employer remits)
- Pag-IBIG contributions (employee share withheld by employer; employer remits)
- Court-ordered deductions or garnishments (e.g., support; lawful writs)
Key compliance point: statutory deductions must be properly computed and remitted. “Withheld but not remitted” can expose employers to serious liability under the relevant agency laws.
B) Union dues and similar “check-off” deductions
Union dues and other check-offs can be lawful when they comply with labor law rules on authorization (typically requiring proper written authorization and observance of union/CBAs and statutory requirements). Employers should not treat “membership” as an automatic license to deduct unless the legal prerequisites for check-off are satisfied.
C) Employee-authorized deductions (voluntary, written, specific)
Many private payroll deductions can be legal if they are:
- voluntary,
- specifically authorized (ideally written and itemized), and
- not a disguised employer benefit, penalty, or kickback.
Common examples:
- loan amortizations (company loan, cooperative, legitimate lending channels),
- insurance premiums with consent,
- contributions to cooperatives/savings plans with consent,
- authorized payments to third parties (e.g., a legitimate financing arrangement), with written authority.
Red flags that often make “authorized” deductions unlawful in practice:
- the “authorization” was a condition for hiring (coerced consent),
- the authorization is a blanket, open-ended authority (“deduct any losses/charges as company deems fit”),
- the deduction funds the employer’s operating costs, penalties, or business losses (not truly for the employee’s benefit),
- the deduction is imposed despite a revoked authorization or without showing the actual basis/amount.
D) Deductions for absences/tardiness/undertime: not a “deduction” in the same sense
Not paying wages for time not worked (e.g., unpaid absences) is generally permissible because wages correspond to compensable work time—subject to rules on paid leaves, holiday pay eligibility, and wage order requirements.
But employers must be careful not to convert this into an illegal penalty, such as:
- “tardiness fines,”
- arbitrary rounding that consistently underpays,
- docking beyond the time actually missed.
5) “Facilities” deductions (meals/lodging) — lawful only under strict rules
Employers sometimes deduct for meals, lodging, or other items provided to employees. Philippine law distinguishes:
- Facilities: items primarily for the employee’s benefit (may be credited/deducted under strict conditions), versus
- Supplements: items primarily for the employer’s benefit or given as part of compensation (generally not deductible).
For a facilities deduction to be defensible, employers typically must show, among other things:
- the employee voluntarily accepted the facility,
- the facility is primarily for the employee’s benefit,
- the value deducted is fair and reasonable (not inflated),
- the arrangement is properly documented and consistent with labor standards guidance and jurisprudence.
If meals are required by the job arrangement, or lodging is mainly for the employer’s operational convenience, treating them as “deductible facilities” is risky and often unlawful.
6) The heart of the issue: “variance” charges
A) What employers mean by “variance”
In many workplaces—retail, F&B, gasoline stations, groceries, pharmacies, warehouses—“variance” refers to:
- cash register shortages (or sometimes overages),
- inventory shrinkage (missing stocks),
- breakage/spoilage,
- sales discrepancies (voids, refunds, wrong pricing),
- discrepancies in remittances versus POS totals.
Many companies then deduct these amounts from:
- daily wages,
- monthly salary,
- commissions,
- incentives, or
- final pay.
B) The legal problem: “variance” often shifts ordinary business losses to labor
Ordinary shrinkage, operational leakage, customer fraud, system errors, and pilferage risks are typically business risks. Philippine wage-protection rules make it difficult for employers to automatically pass these losses to employees through payroll deductions.
As a rule, automatic variance deductions are unlawful unless the employer can bring the deduction squarely within the limited rules on employee liability for loss/damage and comply with due process.
7) When “variance” deductions can be legal (narrow pathway)
A “variance” deduction is most likely to be defensible only when all of the following are true:
1) The loss is specific, actual, and quantifiable
The employer must identify:
- the precise shortage or loss,
- the amount,
- the transaction(s) or incident,
- how the shortage was computed.
Illegal pattern: fixed “variance fees,” percentage-based charges, or pooled amounts not tied to an actual, traceable loss.
2) The employee’s responsibility is clearly established
It must be shown that the employee is actually responsible, not merely present in the workplace when variance occurred.
Factors that tend to support responsibility (not automatically, but contextually):
- the employee had exclusive custody/control (e.g., solo cashier with assigned till; no shared drawer),
- proper turnover procedures existed and were followed,
- access logs/CCTV and audit trails support attribution.
Factors that usually defeat responsibility:
- shared cash drawers / multiple cashiers using the same till,
- weak or nonexistent inventory controls,
- management control over pricing/discount approvals,
- systemic POS issues or unclear audit trails,
- multiple employees with access to stocks/cash rooms.
3) The employee is afforded due process before deduction
Before making deductions for alleged loss/damage attributable to an employee, the employer should give the employee:
- notice of the shortage and basis,
- a meaningful chance to explain/contest (hearing or written explanation),
- an impartial determination of responsibility.
Automatic deduction with no investigation is a major legal vulnerability.
4) The deduction is limited (no profit, no padding, no punitive add-ons)
If a deduction is allowed at all, it should be limited to:
- the actual proven loss attributable to the employee,
- without “processing fees,” “administrative charges,” or punitive multipliers.
Illegal pattern: deductions that include penalties, interest, “service charges,” or forced amortization beyond the proven loss.
5) It must not be a prohibited kickback, deposit scheme, or coercive condition
If “variance” is implemented through any of these, it becomes high-risk or plainly illegal:
- Kickbacks: requiring employees to pay the employer back as a condition of work, or to keep their job.
- Forced deposits/cash bonds: requiring workers to put up deposits that the employer later uses to cover losses, except under narrowly regulated circumstances contemplated by wage rules on deposits for loss/damage.
- Blanket authorizations: “I authorize the company to deduct any variance/losses it deems appropriate,” especially if required for hiring.
8) “Cash bonds” and deposits for loss/damage (often linked to variance)
Some employers try to “solve” variance by requiring:
- a cash bond upon hiring,
- a revolving deposit fund,
- salary withholding “in advance” against future shortages.
Philippine wage rules strongly regulate deposits for loss/damage. As a practical matter, cash bonds are frequently challenged because:
- they are imposed as a condition of employment,
- they function as a blanket guarantee for normal business losses,
- they are not supported by the narrow circumstances and safeguards contemplated by wage regulations,
- employees are not afforded due process before applying the bond.
Even when deposits are used, the employer must still justify any deduction from that deposit with the same rigor: actual loss, employee responsibility, due process, and proportionality.
9) Common “variance” scenarios and their likely legal treatment
Scenario A: Solo cashier, assigned till, end-of-shift shortage
Potentially lawful, but only if:
- exclusive custody is proven,
- audit trail is reliable,
- the cashier is heard and found responsible,
- deduction equals the actual shortage and isn’t padded,
- the deduction is not a disguised penalty.
Scenario B: Shared cash drawer among multiple staff
Generally unlawful to deduct from one (or all) employees without a clear basis allocating responsibility. Pooled deductions are especially vulnerable.
Scenario C: Inventory variance in a store/branch (shrinkage)
Usually not deductible as a payroll deduction because responsibility is diffuse (delivery, stocking, selling, security, management controls). Employers may discipline for proven wrongdoing, but payroll deduction requires a much tighter proof chain.
Scenario D: Breakage/spoilage in restaurants/retail
“Breakage charges” deducted from pay are commonly treated as unlawful, unless the employer proves:
- a specific incident,
- employee fault/negligence,
- due process,
- reasonable limitation to actual damage.
Even then, employers should be cautious: breakage/spoilage can be an ordinary operational risk, and punitive “breakage fees” are legally suspect.
Scenario E: Customer fraud / counterfeit bills / chargebacks
Typically business risk, not automatically deductible. Deductions become more defensible only where there is clear employee fault (e.g., deliberate misconduct or gross negligence proven through due process).
Scenario F: Robbery/third-party theft
Generally not deductible from employees absent clear proof of employee participation or culpable negligence established after due process.
10) Deductions that are commonly illegal, even if labeled “variance”
Employers often attempt these, but they are high-risk or plainly prohibited under wage-protection principles:
- Fines for tardiness, wrong uniform, minor infractions (pay docking as punishment)
- “Administrative charges” added on top of shortages
- Training fees deducted from wages (especially pre-employment)
- Requiring employees to buy uniforms/tools from the employer via deductions without genuine choice
- Deductions for damaged company property without investigation and due process
- Withholding wages to force employees to sign quitclaims or accept liability
- “No remittance, no pay” beyond lawful wage rules (e.g., withholding earned wages to compel turnover)
Discipline may be possible through lawful HR processes, but converting discipline into pay penalties is where wage protection rules bite.
11) Final pay: deductions and “clearance” issues
Upon resignation or termination, final pay is still subject to wage-protection principles. Employers often attempt to withhold final pay due to:
- unreturned company property,
- unresolved variance,
- incomplete clearance.
Legal risk points:
- “Clearance” procedures cannot be used to justify indefinite withholding of wages.
- Deductions from final pay must still be lawful deductions—statutory, employee-authorized, or proven loss/damage with due process.
- A disputed “variance” claim is often better pursued through proper proceedings than by unilateral deductions.
12) Practical compliance checklist
For employers (to keep deductions legally defensible)
Identify the legal basis for every deduction (statute/court order/written authorization/loss-damage rules).
Use specific written authorizations for voluntary deductions; avoid blanket authorities.
For shortages/losses:
- implement tight controls (exclusive custody where applicable),
- keep audit trails and documentation,
- conduct investigation and provide due process before deduction,
- deduct only the actual proven amount attributable to the employee.
Avoid pooled variance charges, percentage “variance fees,” and punitive add-ons.
For employees (to evaluate whether a deduction is lawful)
Request a breakdown: computation, incident details, and basis.
Check whether you signed a specific written authorization.
If it is a shortage/loss claim, ask:
- Was I given notice and a chance to explain?
- Was the cash drawer/shared access controlled?
- Is the amount tied to an actual, documented shortage?
13) Bottom line
Under Philippine law, employer deductions are legal only when they fall within tightly defined categories: statutory deductions, properly authorized voluntary deductions, or carefully proven loss/damage deductions made after due process. “Variance” charges are not automatically lawful just because the company calls them “standard policy.” Where variance is used to routinely transfer operational losses to employees—especially through automatic, pooled, or punitive deductions—it collides with the Labor Code’s wage-protection framework and is highly vulnerable to being declared illegal.