Five Sea Tigers were killed in the intense naval gun battle Thursday, the LTTE said. The body of a SLN trooper was also recovered by the Tigers.
The SLN has listed dozens of sailors as missing.
The clash erupted after the SLN attacked Sea Tiger boats on training exercises off the coast of Nagarkovil in the northern peninsula.
The two Dvora FACs (P461 and P416)were seized and the Sea Tigers dismantled all the armament including a 23 mm cannon and a HK automatic grenade launcher.
A 23 mm Cannon, five PK-LMGs, four 50 calibre guns and an Heckler-Koch Auto Grenade Launcher with ammunition were seized by the Sea Tigers.
On Thursday night reporters in Kilinochchi were allowed to meet the four SLN personnel who were captured by the Tigers.
Meanwhile, Sri Lankan naval officials in Colombo claimed that the Dvora FACs which came under attack east of Point Pedro were escorting a vessel "Green Ocean‚" with 300 people on board.
However, an LTTE spokesman denied the Sri Lankan claim and said there was no ship observed during the clashes.
The clashes took place when Sri Lankan Air Force (SLAF) Kfir jet bombers and helicopter gunships attempted to attack the Sea Tiger vessels, he said.
He also refuted Sri Lankan Navy officials claim that several Sea Tiger boats were destroyed.
The entire LTTE flotilla under the Command of Deputy Commander of Sea Tigers, Cheliyan, safely returned to their base in Vanni with the captured armaments, prisoners and the recovered body, quoted Sea Tiger Special Commander Col. Soosai as saying.
The first Dvora was sunk around 5:30 p.m. Thursday in the seas off Point Pedro as the Sea Tigers pursued a group of SLN vessels that had fired on them.
It was engulfed in a ball of fire, disintegrated into pieces and sank.
Another SLN gunboat was damaged around 6:00 p.m. off Valvettithurai by the Sea Tiger flotilla which chased the surviving SLN vessels into Kankesanthurai harbour, eyewitness reports in Vadamaradchi said.
Two Sri Lanka Air Force (SLAF) Kfir bombers flew overhead attempting to turn back the Sea Tiger flotilla, the eyewitness reports from Point Pedro said.
In a clash at sea near Trincomalee the following day, SLN gunboats destroyed an LTTE boat escorting another boat carrying the body of an LTTE officer, Lt. Col. Arivu, killed in fighting in the Vaharai area earlier this month.
The navy captured the second LTTE boat, but the crew escaped. The SLN handed the body of Lt. Col. Arivu to the International Committee of the Red Cross (ICRC) to be handed back to the LTTE.