Short answer. Yes, but only in defined situations. Article 102 allows payment by check or money order where that manner of payment was customary when the Code took effect, where special circumstances specified in regulations make it necessary, or where a collective bargaining agreement stipulates it.
What the law says
Payment of wages by check or money order shall be allowed when such manner of payment is customary on the date of effectivity of this Code, or is necessary because of special circumstances as specified in appropriate regulations to be issued by the Secretary of Labor and Employment or as stipulated in a collective bargaining agreement.
Labor Code, Article 102 — Forms Of Payment. Read the full provision →
Why this needed express permission at all
The first sentence of the article bars payment of wages in any object other than legal tender. A check is not legal tender; it is an instrument that has still to be presented and honoured. That is the reason the Code could not simply leave checks alone and had to permit them by name. Reading the two sentences together tells you how the provision is meant to work: cash is the rule, the check is a permitted departure, and the departure comes with its own conditions rather than being freely available.
The three gateways
Payment by check or money order shall be allowed when such manner of payment is customary on the date of effectivity of this Code, or is necessary because of special circumstances as specified in appropriate regulations to be issued by the Secretary of Labor and Employment or as stipulated in a collective bargaining agreement. Three routes, and the middle one is not self-assessed: the special circumstances have to be ones the regulations specify. An employer's own judgement that checks are more convenient, or safer than holding cash on the premises, is not one of the gateways the sentence lists.
What the article does not say about bank payroll
The provision names checks and money orders. It does not, in its own words, address crediting wages to a bank or ATM account, which is how most Philippine payrolls now run and which did not exist in this form when the Code was written. That question falls to the regulations the article contemplates rather than being settled by the sentence itself. So if your concern is an ATM payroll arrangement, the useful enquiry is what those regulations require of it — not whether this article names it, because it does not.
The test that usually matters in practice
Whatever route applies, watch what actually reaches you. A check that must be encashed at a distant branch, that carries a fee, that is issued late, or that is dishonoured leaves the wage unpaid in substance however the payroll records read. Keep the checks or advice slips, note the date each was released and the date it cleared, and record any cost or travel involved in converting it to cash. Those details are what turn a general concern about the payment method into something a lawyer can act on.