Mongolia became a member of the International Maritime Organization in 1996, but its engagement with maritime affairs predates this, with ratifications of key conventions such as the Convention on Transit Trade of Landlocked States in 1966, the Barcelona Declaration recognizing the Right to a Flag of States with no Sea-cost in 1976, and the Convention on High Seas. Since then, Mongolia has acceded to over 30 major maritime conventions, aligning its practices with the UN Convention on the Law of the Sea. The country exercises its right to fly the national flag on ships, fulfilling international obligations through flag state control.

Ulaanbaatar was designated as the port of registration in 1996, initiating the ship registration process through government resolution No. 136. The former Minister of Infrastructure Development was tasked with establishing a ship registration port unit, leading to the creation of the "Mongolia Ship Registration" joint company in 2003. This collaboration with the Singapore Maritime Chain company addressed Mongolia's initial lack of management, expertise, and knowledge in maritime transport and ship registration.

Mongolia's legal foundation for waterway and maritime transport was established with the passage of the Maritime Law in 1999, "Procedures for Registering Ships in the Mongolian Ship Register" in 2003, and the Law on Waterway Transportation in 2003. In response to the 2007 amendments to the Maritime Law, the Maritime Administration gained independence and underwent organizational changes.

The Maritime Administration, now reporting to the Ministry of Road and Transport Development, operates under an authorized organizational structure. An audit conducted by the International Maritime Organization (IMO) in November 2016 highlighted the need for Mongolia to strengthen its legal framework, incorporate international standards into domestic legislation, increase qualified personnel, and improve the inspection system for registered ships.

The Government Resolution No. 201 in 2018 approved a strategic plan to implement conventions and agreements agreed upon by Mongolia in the maritime industry. The Maritime Law was revised in accordance with international standards and IMO audit recommendations, receiving approval from the State Great Khural in 2017. Amendments to the Law on Water Transport in 2017 further underscore Mongolia's commitment to ensuring the registration, technical use, and safety monitoring of water vehicles.

Currently, the Mongolia Maritime Administration (MMA) focuses on implementing international and domestic maritime laws and regulations, overseeing ship registration, managing maritime transportation, optimizing dry and sea port utilization, monitoring domestic waterway transport, and training national professionals in the maritime field.