Short answer. The System decides first. Article 180 gives it original and exclusive jurisdiction over disputes on coverage, entitlement to benefits, and contributions, subject to appeal to the Commission — which is required to decide an appealed case within twenty working days from the submission of the evidence.
What the law says
The System shall have original and exclusive jurisdiction to settle any dispute arising from this Title with respect to coverage, entitlement to benefits, collection and payment of contributions and penalties thereon, or any other matter related thereto, subject to appeal to the Commission
Labor Code, Article 180 — Settlement Of Claims And Appeal. Read the full provision →
The first decision is not a court's
Article 180 places these disputes in one place to begin with: The System shall have original and exclusive jurisdiction to settle any dispute arising from this Title with respect to coverage, entitlement to benefits, collection and payment of contributions and penalties thereon, or any other matter related thereto, subject to appeal to the Commission. Exclusive means what it says. A worker who feels a claim has been wrongly refused does not start by suing; the argument belongs, at the outset, to the body that administers the scheme, and going elsewhere first usually costs time rather than saving it.
How wide 'any dispute' reaches
The listed subjects cover most of what actually goes wrong. Whether you were covered at all on the day of the contingency. Whether what happened entitles you to benefits. Whether contributions were paid, by whom, and with what penalties. And then the catch-all — any other matter related to the Title. So an argument that your employment was never reported, or that the contingency did not arise from your work, is decided within this framework rather than treated as a separate species of case.
The appeal, and the twenty working days
A denial is not the end. The article makes the System's determination subject to appeal to the Commission, which is directed to decide appealed cases within twenty working days from the submission of the evidence. Read that period carefully, because it runs from when the evidence is in, not from when the appeal is lodged. A case that sits incomplete does not start the clock, which is a practical reason to file everything you intend to rely on at once rather than in instalments.
What tends to decide an appealed claim
Documents, mostly. The medical records and their dates, showing what the condition is and when it appeared. The employer's report of the incident, and whether it matches what happened. Proof of what your work actually involved day to day, which is often what connects the condition to the employment. Your employment record and proof of coverage. Where a denial cites a specific reason, answer that reason directly with evidence, and keep a copy of everything filed and the date it was received.