Bello Dukku said by telephone that the dead also included at least 15 soldiers and a few civilians.
Dukku said he had had to leave the morgue after counting 100 bodies, because of the overwhelming stench. He said another 50 people had been injured in the fighting.
Government and security sources say troops were fighting on Monday with air support to recapture the northeastern town of Monguno from Boko Haram insurgents as more than 5,000 residents fled.
The insurgents on Sunday seized the town, which lies on the shores of Lake Chad, in a triple offensive that also targeted Konduga and the outskirts and airport of the main northeastern city of Maiduguri, the birthplace of Boko Haram’s five-year-old insurgency, which it covets as the potential capital of an Islamic state.
The conflict with Boko Haram has intensified in the past year and is a major issue in the campaign for a presidential election on Feb. 14 that pits President Goodluck Jonathan against former military ruler Muhammadu Buhari.
Defence spokesman Major-General Chris Olukolade said on Sunday evening that warplanes had attacked rebel positions after ground troops were forced to retreat. Soldiers said they had come up against superior firepower.
On Monday, a security source said the bombardment had resumed.
Monguno lies near the larger town of Baga, which was seized by Boko Haram this month along with a military base in an attack that left scores of civilians dead.
In a video claiming responsibility for the capture of Baga, the insurgents said they had seized enough weapons to “annihilate Nigeria”.
A spokesman for the National Emergency Management Agency (NEMA), Abdulkadir Ibrahim, said over 5,000 people had been registered as having fled Monguno.
He said a housing estate still under construction had been converted into an emergency refugee camp.
In a visit to Nigeria on Sunday, U.S. Secretary of State John Kerry said the United States was committed to helping Nigeria fight Boko Haram, but its ability to do so would hinge on how well the election was conducted.