Short answer. Yes. Article 290 of the Labor Code sets a flat three-year prescriptive period for offenses penalized under the Code and its implementing rules, without singling out the employer or the employee as the offender. Whoever commits the violation, the same three-year clock applies — except for unfair labor practices under Book V, which carry their own one-year period instead.
What the law says
Offenses penalized under this Code and the rules and regulations issued pursuant thereto shall prescribe in three (3) years.
Labor Code, Article 290 — Prescription Of Offenses. Read the full provision →
The three-year rule is stated without a named offender
Article 290 says that offenses penalized under this Code and the rules and regulations issued pursuant thereto shall prescribe in three (3) years. Nothing in that sentence limits the rule to offenses committed by one side of the employment relationship. The article speaks generally about offenses under the Code, so a violation the Code penalizes prescribes in three years whether the person who committed it is the employer or the employee, so long as it is an offense the Code or its implementing rules actually penalizes.
The one exception the article carves out
Article 290 treats one category differently: all unfair labor practice arising from Book V shall be filed with the appropriate agency within one (1) year from accrual of such unfair labor practice; otherwise, they shall be forever barred. Unfair labor practice claims get a shorter, one-year window rather than the general three years. This exception is defined by the type of offense, not by who committed it, so it applies the same way regardless of which party is accused of the unfair labor practice.
What the article does not itself list
Article 290 does not enumerate which specific acts count as offenses under the Code, nor does it separately identify offenses that only an employer can commit versus ones only an employee can commit. It simply fixes the prescriptive period once something is established as an offense penalized under the Code or its regulations. Whether a particular act actually qualifies as such an offense is a separate question this article does not answer. Two features of the wording are worth drawing out. The period covers offences penalised under the Code and the rules and regulations issued pursuant thereto, so the source of the duty breached may be an implementing regulation rather than a provision of the Code itself. And the one-year rule is expressly confined to unfair labour practice arising from Book V — a Book V matter that is not an unfair labour practice is not put on the shorter clock by that sentence.
Two sentences that are not built the same way
The two periods are also phrased differently, and the difference is not cosmetic. The first sentence says offences shall prescribe in three years — it speaks about the offence itself lapsing. The second imposes a filing deadline: the unfair labour practice shall be filed with the appropriate agency within one (1) year from accrual, and otherwise is forever barred. One describes an offence dying of age; the other describes a door closing on a claim, in unusually absolute language. What Article 290 does not supply, in either sentence, is a definition of when the period begins to run beyond the word accrual, or any statement about what might interrupt it once running. Those are exactly the points on which a dispute about a stale complaint tends to turn, and the article leaves them to be worked out elsewhere rather than answering them itself.