At least 35 people were killed when Nigerian soldiers opened fire after a bomb blast struck their convoy in the northeastern city of Maiduguri.
Staff at 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.
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.
A security spokesman 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.
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.
A crackdown on the group this year has had mixed results, weakening it but also pushing it into new areas south of its heartland.