"Failure to hold members of the security forces to account for abuses has emboldened them to commit serious crimes without fear of being brought to justice," he told the AFP news agency.
But Emmanuel Ojukwu, a national police spokesman, dismissed accusations that the police response to the Boko Haram attacks was heavy-handed.
"They were making bombs, they attacked many police stations, they killed many people and they held many hostages," Ojukwu told Al Jazeera.
"No responsible government will allow that to happen in any part of the world.
"They were out bombing police stations and bombing government infrastructure. All the police and security forces did was to restore order and normalcy."
Nigerian officials announced earlier in the day that Yusuf had been shot dead by police as he attempted to flee his compound in the northern city of Maiduguri.
"Mohammed Yusuf was killed by security forces in a shootout while trying to escape," Moses Anegbode, a police assistant inspector-general for northeastern Nigeria, told the local BRTV state television.
"I can confirm that he has been killed and the body is with us."
State television footage shown to officials and journalists showed jubilant police celebrating around the body.
But a Reuters news agency reporter and other local journalists said they had seen Yusuf at a military barracks in Maiduguri standing up and with no visible injuries following his capture.
He was then transferred to the city police headquarters where he died.
A BBC correspondent said a video shown to officials and journalists showed Yusuf confessing and saying he regretted his actions.
"The next moment on the video footage he was seen shot ... They showed his body," the correspondent said.
Al Jazeera's Yvonne Ndege, reporting from inside the compound in Maiduguri, said police said Yusuf's death followed a fierce gun battle between Nigerian security forces and Boko Haram members.
"It really is an unbelievable sight. It looks like a complete war zone," Ndege said.
"Everywhere you look you can see human body parts poking out of rubble, out of branches, out of trees.
"It's been a terrible incident for people living in and around Maiduguri."
The gun battle followed days of deadly violence between Boko Haram members and security forces in which hundreds of people were killed.
The Nigerian Red Cross said authorities had collected more than 200 bodies from the streets of Maiduguri alone.
But Ndege said authorities do not believe the violence is over.
"The governor of Borno state said that [authorities] are concerned about the possibility that Boko Haram militants had fled Maiduguri," she said.
"They could possibly be regrouping in other parts of Borno state and the other states that have been affected by the violence.
"Members of the public are being told to stay at home."
Boko Haram, which means "Western education is prohibited" in the local Hausa dialect, has called for the enforcement of sharia, or Islamic law, including among non-Muslims.
The clashes began on Sunday in nearby Bauchi state, with Boko Haram fighters attacking police stations, before they spilled over into neighbouring states.
But most of the casualties appear to have been in Maiduguri, the northeastern city known as the birthplace and stronghold of the group.
Nigeria's 140 million people are nearly evenly divided between Christians, who dominate the south, and the primarily northern-based Muslims.
Islamic law was implemented in 12 northern states after Nigeria returned to civilian rule in 1999 following years of military rule.