It said ground troops captured "Munagam Base," situated six kilometers (four miles) north of the frontlines in the Weli Oya region, on Thursday.
"The base had been used by terrorists as a back-up to launch attacks on troops," the ministry said.
The ministry, whose claims cannot be verified due to a ban on reporting from frontline areas, said other clashes in the Vavuniya area in the north also left four Tiger rebels dead and government five soldiers injured.
There was no immediate comment from the Liberation Tigers of Tamil Eelam (LTTE), who are fighting for a separate homeland for minority Tamils from the majority Sinhalese community.
Thursday's fighting raises to 3,954 the number of rebels the government says it has killed since January. The ministry says 300 soldiers have died over the same period.
Fighting has escalated sharply since Colombo pulled out of a Norwegian-brokered ceasefire in January.
Tens of thousands have died on both sides in over three decades of bloods