Police commissioner Abdu Umar linked the attack in Dikwa to Boko Haram insurgents. He said a policeman was killed in a separate incident.
Bulama Modu, a resident who assisted the military in recovery work, said a total of 33 fishermen had been killed. He said 25 bodies were found at the scene of Wednesday's attack while eight others were recovered on Thursday.
Another resident who escaped said the insurgents suspected that fishermen were providing information to the military after the army attacked them some weeks ago. The insurgents extort levies from the fishermen.
The military did not respond to a request for comment.
Dikwa is close to the Sambisa forest, a Boko Haram stronghold, which has been fought over by Islamic State West Africa Province, who are also active in the area.
The Boko Haram insurgency, which erupted in northeast Nigeria in 2009, has killed more than 350,000 people and forced millions to flee their homes.