The nurses in the Umaru Shehu hospital said 30 of the dead were in civilian clothes, while another five wore military uniforms. Militants of the Boko Haram Islamist sect, headquartered in Maiduguri, sometimes wear civilian clothes.
"They brought in so many dead bodies. They were more than 30 civilians, in civilian dress. We counted five dead soldiers as well," a nurse, who declined to be named, said. Most had died of gunshot wounds, she added.
Boko Haram is waging an insurgency against President Goodluck Jonathan's government with the avowed aim of reviving an ancient Islamic kingdom in majority Muslim northern Nigeria.
Styled on the Afghan Taliban, the sect's purported leader Abubakar Shekau has said he wants to impose sharia, Islamic law, on the country of 160 million people, around half of whom are Christians and the other half Muslim. His movement has become the number one security threat to Africa's top energy producer.
Borno state security spokesman Sagir Musa said he could not confirm or deny the casualty toll, but he admitted troops had opened fire after a bomb they suspected to be remotely detonated wounded two of them in a patrol.
He said the military would give a statement on Wednesday morning.
Nigerian forces launched a fresh operation against Boko Haram over the weekend, killing 30 of its members, including a senior commander, and arrested 10 others in a raid on the northeastern city of Damaturu, they said on Monday.
A crackdown on the group this year has had mixed results, weakening it but also pushing it into new areas south of its heartland. Northerners complain that heavy-handed police and military tactics, including indiscriminate killings and arrests, have made new recruits for the sect.
Lieutenant Eli Lazarus, a spokesman for joint military and police forces in northeastern Yobe state, said in a statement that they had conducted cordon and search operations at a suspected Boko Haram hideout in Damaturu on Sunday and "engaged in a gun battle with the suspected terrorists".
"About 30 suspected Boko Haram terrorists were killed in the battle which lasted several hours ... The notorious one-eyed Bakaka, the field commander of Boko Haram in Damaturu and a close associate of Abubakar Shekau, was killed," he said.
Ten others were arrested and "are presently assisting investigators to track other senior members of the terrorist group", he added. Three homemade bombs, six assault rifles, 90 rounds of ammunition and several knives were seized, he said.
There was no immediate comment from Boko Haram.