Nigerian Islamic sect leader Mohammed Yusuf was alive when he was captured, the commander of the operation against the militant group has told the BBC.
The comments by Col Ben Ahanotu appear to contradict police statements that Mr Yusuf, 39, was killed in a shootout as he was being detained.
Human rights campaigners have alleged Mr Yusuf was executed by the police.
Mr Yusuf's Boko Haram group has been blamed for days of violent clashes with security forces in which hundreds died.
His bullet-riddled body was shown to journalists on Thursday just hours after police said they had captured him in the northern city of Maiduguri.
Col Ahanotu, the commander of the operation against the Boko Haram group, said he had personally captured Mr Yusuf and handed him over to the chief of police.
He said Mr Yusuf had been unarmed when caught, hiding in an empty building a short distance from his enclave, and that he gave himself up willingly.
"All I know is that in the attack, I was able to pick him up from his hide out and hand him over to police," he told the BBC.
"I asked him why he did what he has done and his response was that he would explain to me later."
Col Ahanotu said Mr Yusuf had a wound on his arm which had already been treated.
"But he was OK. As I got him alive, I handed him over to the authorities," he said.
Officials visit Maiduguri to see the damage left by days of fighting
Nigeria's Information Minister Dora Akunyili told the BBC that how Mr Yusuf had died was "a big issue to the good people of this country because Nigeria believes in the rule of law, Nigeria believes in fundamental human rights being respected".
She said his death would be investigated but that the security agencies should be "commended for being able to bring to a stop this killing and destruction in just a few days".
Ms Akunyili also defended her earlier comments that the death of Mr Yusuf - who she described as being a leader "in the mode of Osama Bin Laden" - demise was "positive" for Nigeria.
She said if he had not been stopped the violence would have spread to other states in the north of the country.
Regional police assistant inspector-general, Moses Anegbode, had earlier told Nigerian television Mr Yusuf had been "killed by security forces in a shoot-out while trying to escape".
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.