The Food Safety Commission (FSC) is an independent government coordinating body which reports to the MfH. The FSC is responsible for risk management and risk communication. The FSC is the coordination office for issues related to food safety and provides a forum for cooperation between the MAFA, MfH and the Malta Competition and Consumer Affairs Authority (MCCAA), as well as other entities involved in food safety. The FSC is responsible for the registration of all food establishments.

In Malta, the Public Health Laboratory is the National Reference Laboratory pursuant to Regulation (EC) No. 882/2004. It draws on the services of National Reference Laboratories in other EU Member States.