The governor criticised the army's show of force in dealing with members of the group and its leader.
The governor decried the army's show of force in dealing with agitators in the region, drawing comparisons with how the Arewa groups in the north were treated after they threatened Igbo residents in the northern region.
Fayose issued his condemnation of the government's approach through his Twitter account (@GovAyoFayose), on Thursday, September 14, 2017.
He tweeted, "For whatever reasons, the Federal Government should have allowed the Southeast governors to interface with Kanu and resolve issues instead of this show of force.
"If Northern governors were allowed to resolve the Arewa Youths threat that the Igbos should leave the North, why not allow Southeast governors to resolve Kanu's?"
On June 6, a coalition of northern youths issued a threatening quit notice warning Igbos living in the northern region of the country to leave before October 1.
The coalition, which includes Arewa Citizens Action for Change, Arewa Youth Consultative Forum, Arewa Youth Development Foundation, Arewa Students Forum and Northern Emancipation Network, promised to execute measures to carry out their directive.
After widespread criticism and months of intervention meetings both by the Federal Government and the governors of the country's 19 northern states, the coalition withdrew the quit notice on Thursday, August 24, at a press briefing at the Transcorp Hotel in Abuja.
In an announcement that was made by the group's spokesman, Abdulaziz Suleiman, it said despite the withdrawal, the group will not relent in pursuing petitions to the United Nations and the Federal Government to sanction Indigenous People of Biafra (IPOB) leader, Nnamdi Kanu, and other IPOB sponsors for their disruptive activities.
In contrast to the treatment of the threat from the northern group, deployment of soldiers in the South-East has led to clashes this week with members of IPOB.
A detachment of the Nigerian Army had been present around the home of the IPOB leader on Tuesday, September 12, creating heightened tension with members of the group only days after soldiers clashed with them while trying to gain access to the group's leader's house on Sunday, September 10.
While reports indicated that soldiers had tried to gain access into Kanu's father's compound in Umuahia and shot at IPOB members who formed a human shield to keep them out, the army dismissed the claims and said the soldiers had been attacked with stones while passing through the residence in a new armoured carrier.
While reacting to the incident on Monday, September 11, Kanu accused Chief of Army Staff, Lieutenant-General Tukur Buratai, of trying to incite his group into arming themselves to deliberately provoke a war.
He said, "Nigeria is bringing war to us, we're not fighting anybody. It is Buratai and his men that are bringing war unto us.
"They want us to become armed so that the world can say that Nnamdi Kanu is leading a violent armed group, which is not the case. They're provoking us to war."
The clashes between the opposing sides led to state governor, Okezie Ikpeazu, declaring a dusk to dawn curfew that has been extended till Friday, September 15.