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MMEA was formed as a result of a study undertaken by the Malaysian government in April 1999. The study revealed that enforcement was not effective because too many agencies were involved that resulted in overlapping functions, overlapping jurisdiction, and uneconomical use of resources.

The MMEA began with the creation of a Nucleus team, tasked with making the necessary efforts in the establishment of the agency. The agency was formally established with the enactment of the Malaysian Maritime Enforcement Agency Act 2004. Subsequently, the Act was gazetted on 1 July 2004 and came into force on 15 February 2005. The agency achieved operational status on 30 November 2005 with a soft launch. MMEA was officially launched by the Hon. Deputy Prime Minister of Malaysia on 21 March 2006.