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

The Navy consists of the Warship Flotilla, the Sea Coastal Surveillance System, the Explosive Ordnance Disposal (EOD) Divers Team, the Naval Logistic Service, Training Center and Maritime Rescue Coordination Center. The Flotilla is the core component of the Navy, and consists of the Frigate, the Mine Countermeasures Squadron, the Patrol Ships Squadron, and the Harbour Boats Group. The Navy's personnel strength is currently more than 600 officers, NCOs, junior ratings and civilian employees.

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

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

The principal development guidelines of the Lithuanian Navy are: upgrading the existing fleet; boosting MCM capabilities; host nation support at the Klaipeda Seaport facilities; the further development of sea and coastal surveillance.