Short answer. To the labour department. The Labor Code directs the appropriate agency of the Department of Labor and Employment, or its authorised representative, to investigate any violation of an apprenticeship agreement — either upon the complaint of an interested person or on its own initiative.
What the law says
Upon complaint of any interested person or upon its own initiative, the appropriate agency of the Department of Labor and Employment or its authorized representative shall investigate any violation of an apprenticeship agreement
Labor Code, Article 65 — Investigation Of Agreement Violations. Read the full provision →
The investigation does not depend on you filing
The article says the agency shall investigate upon complaint of any interested person or upon its own initiative. Both halves are useful. The department may look into a programme without anyone complaining, which matters where the apprentices are young or where nobody wants to be the person who spoke up. And a complaint may come from any interested person — a phrase wider than the apprentice himself, and wide enough to cover a parent who signed the agreement on a minor's behalf.
What counts as a violation is set by your agreement
The subject of the investigation is a violation of an apprenticeship agreement, so the agreement is the measure. Training that was promised and never delivered, an occupation different from the one named, a term extended beyond what was agreed, or conditions that depart from the document all sit inside that description. This is why the written agreement matters so much: without it there is little to compare the employer's conduct against, and a complaint becomes one account of events against another.
The procedure comes from the implementing rules
The article establishes that there is an investigation and who conducts it. It does not set out forms, periods or the steps that follow, because it directs that this be done pursuant to such rules and regulations as may be prescribed by the Secretary of Labor and Employment. So the how is administrative and it changes. Anyone telling you there is a fixed deadline or a particular form required by the Labor Code itself is describing a rule from somewhere else — worth checking against the current issuance rather than taken on trust.
What to have ready before you go
Bring the apprenticeship agreement and any training plan or schedule, a record of what you were actually made to do and when, whatever you were paid, and the names of the people who supervised you. Dates matter more than adjectives. If the arrangement may not really have been an apprenticeship at all — no training, ordinary production work throughout — say so plainly, because that changes what is being complained about and may put the matter before a different forum. A lawyer can tell you which.