Here’s a practical, all-in-one legal explainer—Philippine context—on the deadline (prescriptive period) and process for filing a DOLE complaint over withheld salary. This is general information, not legal advice.

The short answer

Deadline: As a rule, money claims arising from an employer-employee relationship (e.g., unpaid/withheld wages, overtime, holiday pay, 13th-month pay, wage differentials, final pay) must be filed within three (3) years from the date each amount fell due and remained unpaid.
If your dispute includes illegal dismissal: the reinstatement/illegal dismissal aspect generally prescribes in four (4) years from dismissal; the unpaid wages/benefits part still follows the 3-year rule.

Key point: Each missed payday has its own 3-year clock. Older paydays can expire while newer ones remain claimable.

What counts as “withheld salary”?

Unpaid regular wages (daily, weekly, semi-monthly, monthly) that became due but weren’t paid.
Unremitted statutory pay: overtime pay, rest day/holiday premium, night shift differential, service incentive leave (SIL) conversion, 13th-month pay, wage order increases/differentials, and similar labor-standards benefits.
Final pay not released after separation. (DOLE policy guidance expects release within 30 days from separation; failure can support a claim.)

When does the 3-year clock start?

Accrual happens when payment is due but not made.
- Example: Semi-monthly salary covering Sept 1–15 is due on Sept 30 under your payroll cycle. If unpaid, the claim for that tranche normally prescribes three years after Sept 30.
Continuing underpayment (e.g., below-minimum wage) still accrues per payday; count 3 years from each affected due date.

What can pause or interrupt the deadline?

Under Philippine civil-law rules on prescription, any of the following typically interrupt prescription, meaning the clock stops and may reset:

Filing a case/complaint with DOLE or the NLRC/Labor Arbiter.
A written extrajudicial demand from the worker (e.g., demand letter/email asking for payment).
Written acknowledgment of the debt/obligation by the employer.
Filing a SEnA Request for Assistance (the mandatory conciliation step, see below) is widely treated as interrupting/tolling prescription because it is, at minimum, an extrajudicial demand and part of the formal process.

Tip: Keep proof—timestamped email, courier receipt, or DOLE SEnA RFA stub.

Where to file and who handles what

Step 1 — SEnA (Single-Entry Approach) at DOLE.

Mandatory first stop for most labor disputes. You file a Request for Assistance (RFA) at the DOLE Field/Provincial/Regional Office where you worked or where the employer is located. A DOLE officer facilitates a conciliation-mediation conference (usually within 30 days).
If settled, a compromise agreement is executed and enforceable.

Step 2 — If no settlement, venue depends on your claim:

Labor Arbiter (NLRC): money claims regardless of amount and cases involving dismissal/reinstatement, damages, attorney’s fees, and most adversarial disputes.
DOLE Regional Director (Summary Procedure): limited money claims (classically up to ₱5,000 per employee and without reinstatement)—a narrow route; in practice, most substantial unpaid-wage disputes go to the Labor Arbiter after SEnA.
DOLE Labor Standards/Inspection (Visitorial & Enforcement): when a DOLE inspection finds violations, DOLE may order compliance (amount not limited by ₱5,000) without a full-blown NLRC case.

Practical route for withheld salary: File SEnA at DOLE. If unresolved and you’re claiming significant amounts or there’s dismissal/constructive dismissal, proceed to the NLRC Labor Arbiter via a formal complaint (which SEnA can “refer” you to).

What to prepare (evidence checklist)

Bring what you have; lack of payslips is not fatal if other proof exists.

Identity & employment proof: government ID; company ID; contract/appointment letter; onboarding emails.
Pay evidence: payslips, payroll emails, bank statements, ATM passbook/transaction history, cash vouchers, remittance slips.
Time/work proof: timesheets, biometrics logs, schedules, screenshots, task trackers, work emails/chats.
Communications: messages demanding payment; HR replies; HR policies/handbooks; separation papers; clearance forms.
Computation sheet: list every unpaid period, rates, and your totals.

How to compute your claim (quick framework)

Identify each unpaid item and date due (per payday or benefit schedule).
Apply statutory rates where relevant:
- Overtime: beyond 8 hours/day (basic hourly rate × OT premium).
- Night Shift Differential: 10% of basic hourly rate for work from 10:00 p.m. to 6:00 a.m.
- Holiday/Rest Day Premiums: per latest wage rules applicable to your region.
- Service Incentive Leave conversion: unused SIL (if entitled) × basic daily wage.
- 13th-Month Pay: 1/12 of basic salary earned within the calendar year (exclusions may apply per PD 851 rules).
Wage order differentials: if the regional minimum increased during your tenure and you were paid below it, compute the shortfall per day.
Totals + legal interest: if adjudged, legal interest may be imposed from the time of demand or filing until full payment (rate depends on period; adjudicators apply prevailing jurisprudence).

Common scenarios & deadlines

A. Still employed; some paydays unpaid

File SEnA soon. Each unpaid payday has its own 3-year period. Do a written demand now to interrupt prescription.

B. Resigned or terminated; final pay not released

Claims for unpaid salary, pro-rated 13th month, SIL conversion, last-day pay, etc., 3 years from when each item became due. If illegal dismissal is alleged, 4 years for the dismissal relief; 3 years for the money components.

C. Underpaid (below minimum wage)

Compute the daily shortfall × days worked within the last 3 years (older periods may be time-barred).

D. Illegal deductions/“cash bonds”

Treated as money claims → 3 years from each deduction.

E. Government employees

Typically not under DOLE/NLRC jurisdiction; governed by Civil Service rules. Deadlines and venues differ.

F. Overseas workers/seafarers

Special statutes and standard contracts apply; jurisdiction is usually the NLRC after SEnA. Three-year limits commonly apply to money claims, but check the specific contract/statute.

The SEnA pathway (what to expect)

File RFA (walk-in or online, where available).
SEnA conference scheduled; mediator works toward settlement.
If settled: sign a compromise; employer pays per agreement.
If not settled: mediator issues a referral to the proper forum (often NLRC). Your filing date and RFA help show interruption of prescription—keep the documents.

Practical tips to protect your claim

Don’t wait. Even if you want to keep the job, you can send a polite written demand (email is fine) to stop the clock.
Document everything now—pull bank statements and screenshots while you still have access.
Compute by tranche (per payday) so it’s easy to cut off amounts that may have prescribed.
Mind the forum: If your case involves reinstatement/constructive dismissal or large claims, expect NLRC after SEnA.
Group claims: Multiple employees may file together for efficiency, but prescription is individualized—each person’s dates matter.
Beware of releases/quitclaims: These are not automatically valid; coercion, lack of full payment, or unconscionable amounts can invalidate them, but don’t sign lightly.

Sample demand email you can adapt

Subject: Demand for Payment of Withheld Wages and Benefits

Dear [HR/Payroll/Manager], I am writing to demand payment of my unpaid wages and statutory benefits, which have become due and remain unpaid, as follows: – Salary for periods: [list dates and amounts] – [Overtime/Night Diff/Holiday Pay/13th Month/SIL conversion/etc.]: [dates and amounts] Total provisional computation: ₱[amount].

Kindly release the above amounts within five (5) working days of receipt. This serves as a formal demand and notice that I will seek relief through DOLE/SEnA and, if necessary, the NLRC.

Sincerely, [Name, position, contact details]

(Keep a copy and proof of receipt.)

FAQs

1) If my employer pays part of the claim later, does it affect prescription? Partial payment or written acknowledgment of liability generally interrupts prescription for the acknowledged portion.

2) Can I recover older than 3 years if the employer hid records? As a rule no; but inspection findings and certain equitable doctrines can help prove what remains within the last 3 years. Preserve any proof you control.

3) Do I need a lawyer at SEnA/NLRC? Not required, but helpful—especially for sizable or mixed claims (e.g., dismissal + wages). You can appear pro se (self-represented).

4) Will complaining risk retaliation? Retaliation can itself be unlawful. Document any adverse acts following your demand/SEnA; you may add claims if needed.

One-page checklist (save this)

List every unpaid/underpaid period with due dates.
Three-year count from each due date; mark any that may have lapsed.
Send written demand (interrupts prescription).
File SEnA RFA at DOLE.
Prepare evidence (IDs, payslips, bank statements, timesheets, emails).
If unresolved, file at NLRC (or proper forum per advice).
Track legal interest and update computation.

If you want, tell me the dates and amounts that were unpaid, your pay cycle, and your region, and I’ll draft a computation sheet you can use for SEnA or NLRC.