Speaking at a landmark cabinet meeting in the country's Kurdish region on Sunday Maliki said the region is facing a new storm of sectarianism and political challenges in many of the countries, each with different reasons.
He referred to latest wave of violations in Iraq and said “the most dangerous threat now is return of extremists”.
“Unfortunately we are gradually getting infected from the crisis which has gripped the region,” he added and called for respect among different groups in regional countries and hoped for cooperation and friendship.
Violence meanwhile has been rising to levels not seen since 2008 as the government has struggled to head off months of protests, which analysts say has given militant groups fuel and room to maneuver on the ground.
Following Sunday's cabinet meeting, Maliki said he and Kurdish regional president Massud Barzani did "not have a magic wand to fix all these problems in one go."
"But it is necessary to have a willingness to solve them," Maliki said in a joint news conference with Barzani, with whom he has traded harsh words in recent years.
The Iraqi premier said the Arbil talks would be followed by further visits by both sides.
Barzani, meanwhile, said the cabinet session marked "an important visit" and described it as a "start for removing all the problems."
The cabinet session was followed by talks between cabinet ministers and Kurdish regional ministers and a direct meeting between Maliki and Barzani.