The BBC has obtained a photograph which shows that Mohammed Yusuf, the leader of the Boko Haram sect in Nigeria, was alive when captured by the army.
They handed him over to the police. A few hours later, journalists were shown his bullet-ridden body.
The police said he had been fatally wounded while trying to evade capture.
Mr Yusuf's Islamic sect is blamed for days of violent clashes with security forces across northern Nigeria, which killed hundreds of people.
Human Rights Watch in Nigeria have called for an immediate investigation into the killing of Mr Yusuf, 39, which they called "extrajudicial" and "illegal".
On Friday, the army commander of the operation against the Boko Haram group, Col Ben Ahanoto, said he had personally captured Mr Yusuf and handed him over to the chief of police in Maiduguri, the capital of Borno state.
He said Mr Yusuf had a wound in his arm - which is clearly shown in the photograph - which had already been treated.
The police, however, insisted he had been fatally wounded in combat.
The police commissioner of Borno state, Christopher Dega, said Mr Yusuf "was in a hideout, and the forces went there and there was an exchange of fire".
"In the course of that confrontation, he sustained his own injury. He was picked up and he later couldn't make it."
Earlier, police sources had offered a different version of events, saying Mr Yusuf was killed while trying to escape from custody.
Meanwhile, another group of women and children, abducted by the Boko Haram sect, has been rescued from a locked house in Maiduguri.
Officials said the latest group of 140 was in a deplorable condition, suffering from pneumonia, fever and rashes.
Last week, the police rescued about 100 young women and children from a house on the edge of the city. Many said they were the wives of sect members, and had been forced to travel to Maiduguri from Bauchi state.
The BBC reporter in Maiduguri says the Boko Haram sect believed that their families should accompany them to the battlefield.
Hundreds of people were killed in Maiduguri alone during violent clashes between police and the Islamic sect.
Col Ben Ahanotu, head of security in Maiduguri, said that mass burials had begun there.
The Boko Haram compound, he said, was being used as one of the burial sites because bodies were decomposing in the heat.
Life in the affected areas is now beginning to return to normal with banks and markets reopening.
Maiduguri is the capital of Borno state but the fighting spread to cities across the north of the country and the total number of dead is unknown.
A military spokesman said two of those killed were soldiers and 13 were police officers.
The number of injured, meanwhile, is still being counted. The Red Cross had earlier said about 3,500 people fled the fighting.
The violence ended on Thursday with the death of Mr Yusuf.