Two Tamil Tiger boats were destroyed on Saturday off an island, killing six rebels, a naval spokesman said, the second military engagement at sea in less than 24 hours.
On Friday, the navy destroyed seven Tamil Tiger craft in a major sea battle, killing at least 35 rebels off the northern Jaffna peninsula.
Saturday's clash took place near the government-controlled Kytes island off the Tamil-dominated peninsula after navy patrol boats spotted rebel craft approaching the island.
"All six LTTE [Liberation Tigers of Tamil Eelam] members on board were killed," Commander D K P Dassanayake said.
The Sri Lankan navy also killed at least 35 Tamil Tiger fighters in an ongoing sea battle in the northern Jaffna region.
A navy spokesperson said: "Sri Lanka navy boats destroyed seven suicide Tamil Tiger vessels in a sea battle, killing at least 35 rebels."We managed to destroy seven boats. The fighting is going on and we are chasing them."
He said two sailors were also wounded in the fight.
The latest clashes come ahead of peace talks between the Tigers and the government on October 28 and 29.
Peace envoys are pushing both sides to stay the course for the planned talks but a surge in violence risks undermining the meeting in Geneva.
Tigers fired mortar bombs at an army base in the eastern Batticaloa district late on Thursday, sparking army retaliation. There were no casualties, the military said.
The continuing violence came as Richard Boucher, the US assistant secretary of state, is visiting the country, where Tamil Tigers have been fighting for an independent homeland since 1983 for the ethnic Tamil minority.
Evan Owen, the US embassy spokesman, said: "Richard Boucher wants to send a message there should be an immediate cessation of violence. It is more important to talk now than ever as Sri Lanka is in danger of going to all-out war."
On Wednesday, the Tigers launched a sea-borne suicide raid on a naval base in the southern city of Galle, losing 15 cadres and killing one sailor, the first such attack on a town in the Sinhalese-dominated south.
Last week, dozens of Tigers and soldiers were killed in battles in the north-east and hundreds of combatants were wounded.
This week a Tiger suicide attack on a convoy in the north-central district, killed around 100 people, mostly sailors.
Security was tight in the capital, Colombo, with soldiers manning checkpoints and using cordon searches to look for suspected Tiger fighters.