The two sides have been locked in combat since 1972, with the Tigers fighting for a separate state for minority Tamils. The 35-year-old ethnic conflict has claimed more than 60,000 lives.
Troops took the "Sea Tiger" base at Silavattura on Sunday following intense fighting in the Mannar district on Saturday, the defence ministry said in a statement.
"The army successfully captured an LTTE (Liberation Tigers of Tamil Eelam) Sea Tiger base, including three boats and a large quantity of anti-personnel mines and detonators," the ministry said.
It said an unspecified number of civilians had fled and sought shelter in schools and a church within the government-controlled area of Mannar.
Security forces seized territory that had been held by the LTTE just south of Mannar on Saturday, military officials said.
"The army is now engaged in consolidation operations to retain control of the area," the defence ministry said.
In a statement, the LTTE said nine people were killed and four in