He also dismissed claims from human rights groups that security forces had been heavy-handed in their response to the clashes.
"The Nigerian armed forces are one of the best trained in the world. They used only minimum force to repress the Boko Haram," he said.
"Those who are claiming the police used maximum force will be allowed to come and testify [at the inquiry]. The police will also be there to testify and give their own account."
About 600 people were killed in days of fighting that began on Sunday in the northern Bauchi state with Boko Haram fighters attacking police stations, before the clashes spilled over into neighbouring states.
Nigerian authorities said the group's leader, Mohammed Yusuf, was killed in a shootout on Thursday by security forces as he attempted to flee his compound in Maiduguri, the scene of the heaviest fighting.
But Al Jazeera's Yvonne Ndege, reporting from Maiduguri, said there were still questions about whether Yusuf is alive or dead.
"The military say he was shot dead at the compound by the army, but promises to show his remains to Al Jazeera have not been delivered on, leading many to wonder whether they got the right man," she said.
"The authorities also deny rumours he was killed in custody by police as human rights organisations allege."
Meanwhile, police said they rescued 230 hostages seized by members of Boko Haram during the fighting.
Fifty-two hostages were freed from a house in Maiduguri, the state capital, police in the northern state of Borno said on Saturday.
"We have so far rescued more than 230 women and children abducted from many parts of the north, particularly Bauchi, Plateau and Katsina States, kidnapped by members of the Boko Haram sect," Isa Azare, a police spokesman, told the AFP news agency.
A total of 120 rescued women and children were returned on Thursday to Bauchi, from where they had been kidnapped before being brought to Maiduguri, he said.
One of the women told the AFP news agency that Boko Haram members had ushered a group of civilians into waiting buses three days earlier and threatened to kill them if they refused.
The woman, a theology student, said: "We asked questions about our mission but we did not get any answers.
"We were only told that we would continue our studies in Maiduguri and be brought back later."
Boko Haram, which means "Western education is prohibited" in the local Hausa dialect, has called for the enforcement of sharia, or Islamic law, in the country, including among non-Muslims.
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.