A navy spokesman said on Friday that a patrol detected the rebel boats around 6am in the outer harbour of the northeastern port of Trincomalee.
Commander DKP Dassanayake said: "The boats were mingling with dozens of boats of fishermen who normally return with their catch early in the morning.
"We destroyed the two boats of the terrorists which were laden with explosives as there were huge sounds," Dassanayake said, adding that each rebel suicide boat was carrying three people.
"All on board the boats were killed."
The incident followed a sea clash on Thursday in the northern waters, where the rebels said they killed at least 26 Sri Lankan sailors. Five rebels were also killed, the insurgents said.
Tamil Tiger rebels also said they had sunk two naval gunboats and captured four sailors in the fierce sea battle.
The Liberation Tigers of Tamil Eelam (LTTE) said on Thursday that they sank two gunboats and damaged a third in close-quarter fighting off the island's northern peninsula of Jaffna and estimated navy losses at 25 killed.
"We did not use any suicide boats," said Rasiah Ilanthiriyan, the LTTE spokesman, denying defence ministry reports that a Tiger boat loaded with explosives rammed a gunboat and sank it and destroyed another.
Meanwhile, Mahinda Rajapakse, the Sri Lankan president, has ordered an investigation into Wednesday's military attack that led to the killings of a large number of civilians in the island's east.
The separatist violence has killed
over 65,000 people
"President Rajapakse expresses his deep sorrow and regret at the senseless loss of life of innocent civilians at Vakarai and condemns the LTTE's tactics of directing long range artillery fire using human shield that led to this tragedy," the government said in a statement.
It said the authorities had been ordered to pay compensation to the affected families and security force commanders were directed to investigate.
Separately, on Thursday, the military said that the Tamil Tigers detonated a roadside bomb, killing two soldiers in northern Jaffna peninsula.
Meanwhile, a human rights group has denounced the shelling of a school by the military on Wednesday which killed at least 23 people and injured scores more. The government said it regretted the attack.
"While we regret this whole episode, we say that national security is utmost," Keheliya Ramukwella, chief government spokesman, told a news conference.
"While we regret this whole episode, we say that national security is utmost"
Keheliya Ramukwella, government spokesman
Scores of civilians had taken refuge in the school in Kithiraveli - a rebel-controlled eastern Sri Lankan village - from fighting between the army and Tamil Tigers when it was hit, a senior Tiger official told The Associated Press.
He said at least 60 civilians were killed and 150 wounded in the attack.
Helen Olafsdottir, a spokeswoman for the European ceasefire monitoring mission, said monitors had counted 23 bodies, mostly of women, children and older people, and were still investigating. Another 137 people were admitted to hospitals, she said.
"Our monitors have visited the impact site and they have been told that as many as 40 rounds of artillery fire had hit the area," she said. She said the monitors did not find any sign of a rebel military installation in the impact area.