The fishing settlements of Devil's Point and Vallaipadu on the island's northwestern shore were used by the rebels to smuggle arms from south India and launch attacks on troops, the military said in a statement.
Troops would now be able to advance on the LTTE (Liberation Tigers of Tamil Eelam) stronghold of Pooneryn, it said.
Government forces say they have recently taken control of the nearby towns of Kiranchi and Palavi following weeks of heavy fighting.
Clashes continued elsewhere in the north on Wednesday, with the defence ministry reporting artillery exchanges across the districts of Mullaittivu, Jaffna and Kilinochchi.
The ministry did not give out casualty details, but said the LTTE suffered major losses.
There was no immediate comment from the LTTE, who have been fighting since 1972 to carve out a homeland for minority Tamils from the majority Sinhalese community.
Fighting has escalated since Colombo pulled out of a truce in January.