"The boat was salvaged on Saturday and four crewmen were rescued, but one officer went missing and his body was recovered only this morning," a military official said on condition of anonymity, adding that the boat had got into trouble in choppy waters.
Rajapakse, who addressed troops at the land and sea parade, vowed not to allow the Tamil Tiger rebels or any other separatist group to create trouble in the ethnically dived nation of 20 million people.
His troops declared an end to 37 years of ethnic bloodshed after killing the top Tamil Tiger leadership in May 2009.
In the north the main opposition ethnic Tamil political party, the Tamil National Alliance (TNA), defied a military ban and staged a remembrance ceremony for those who died in the final battle which also killed Tigers leader Velupillai Prabhakaran.TNA officials said the main memorial event in the town of Vavuniya went off without incident despite army threats to arrest participants. But in the adjoining district of Mannar, police briefly detained mourners.
The military offensive which crushed the Tigers triggered allegations of war crimes. Rights groups said up to 40,000 civilians perished in the last months of fighting, a charge denied by Colombo.