The Lithuanian Navy is tasked with a wide range of missions: protection of national interests in territorial waters and exclusive economic zone, explosive ordnance search and disposal operations, coordination of search and rescue operations and pollution control., support to special operations, control and protection of sea lines of communication. 

The Navy consists of Flotilla, Sea and Coastal Surveillance Service, Harbour Protection and Coastal Defense Unit, Naval Logistics Service, Training Center and Maritime Rescue Coordination Center. Flotilla is the core component of the Navy consisting of the Mine Countermeasures Squadron, the Patrol Ships Squadron, and the Harbour Boats Group. The Navy's personnel strength is currently above 600 officers, NCOs, enlisted and civilian employees.

As part of NATO, Lithuania specializes in MCM operations, sustains and develops capabilities necessary for contribution to the Standing NATO Mine Countermeasures Group 1 and the NATO Response Force (NRF).

The Lithuanian Navy (along with Latvia) contributes its minehunters and a command and support ship to the Baltic Mine Countermeasures Squadron - BALTRON. Its main task is to conduct MCM operations and train crews of the attached Mine Countermeasures Vessels.

The principal development guidelines of the Lithuanian Navy are: upgrading the existing fleet; boosting MCM capabilities; provision of host nation support at the Klaipeda Seaport facilities; further development of maritime situation awareness capabilities.