Nigeria is transferring the peninsula to Cameroon under a World Court order, despite opposition from locals.
A little-known armed Nigerian group opposed to the handover of the territory, said only four of its men had been killed in the raid.
At least one Cameroon soldier was also killed during the clashes.
It was the second attack on Cameroonian positions in Bakassi within a week.
Cameroon's defence ministry said its men had fought off an attack men in three speed boats.
Ebi Dari, a spokesman for the Niger Delta Defence and Security Council (NDDSC), confirmed its fighters were behind the raid.
"It is true our men came under intense gunfire from the Cameroon military, but only four of them were killed and two taken hostage. They also seized one of our speed boats and the arms that were inside," he told Reuters news agency.
The Nigerian forces are due to complete their long-delayed full withdrawal from Bakassi in mid-August to comply with a 2002 court order by the International Court of Justice, which ruled in favour of Cameroon.
Most of the area's inhabitants are Nigerian fishermen and many are opposed to the handover. Some Nigerian politicians also voiced their opposition to the handover last year.
Nigeria reinforced troops on its side of the border after 21 Cameroon troops were killed in Bakassi in November 2007.
Nigerian troops withdrew in August 2006 but the peninsula will remain under Nigerian civil administration until 2008.
Nigeria and Cameroon sought arbitration after a series of bloody clashes in the 1990s.
Bakassi juts into the Gulf of Guinea, an area which may contain up to 10% of the world's oil and gas reserves. It is also rich in fish.
The peninsula has been administered by Nigeria since independence from Britain in 1960.
However, Cameroon based its claim of sovereignty over the region on maps dating back to the colonial era.
Source : BBC News