In the original statement by the navy earlier Monday, four were said to be injured with an additional five missing.
The attack took place in the jurisdiction of Puerto Leguizamo in the Putumayo department near the border of Ecuador. According to a government report, two naval ships were sailing down the river when they were attacked.
These events come at a sensitive time after the rebel group failed on Sunday to deliver two hostages whose release had been promised.
The failure of the operation has been blamed on the FARC for providing the wrong coordinates for the release site of the two men, Salin Sanmiguel and Guillermo Solorzano.
Negotiations to carry out the final phase of the release mission are currently taking place between the government and the Red Cross after the government stated Monday that it had suspended the mission.