"Baghdadi is definitely alive. He is not dead. We have information that he is alive. We believe 99 percent he is alive," Lahur Talabany told Reuters in an interview.
"Don't forget his roots go back to al Qaeda days in Iraq. He was hiding from security services. He knows what he is doing."
The secretive Islamic State leader has frequently been reported killed or wounded since he climbed up to the pulpit of a mosque in Mosul in 2014 and declared a caliphate with himself the leader of all Muslims.
After leading his fighters on a sweep through northern Iraq, Baghdadi attempted to create a self-sustaining modern-day caliphate in parts of Iraq and Syria.
He is now a man on the run, but still a cunning foe, said Talabany, who as part of the international coalition against Islamic State has been at the forefront of efforts to track Baghdadi down.
"He is not an easy figure. He has years of experience in hiding and getting away from the security services," Talabany said.
"The territory they control right now, still to this day, is very tough territory. It is still not the end of the game for ISIL. Even though they have lost almost all of Mosul and they are getting ready to lose Raqqa as well."
Iraqi security forces have ended three years of Islamic State rule in the Iraqi city of Mosul, and the group is under growing pressure in Raqqa - former strongholds in the militants' crumbling caliphate.
Talabany said Islamic State was now shifting tactics despite low morale and it would take three or four years to eliminate the group as it takes to the mountains and deserts to stage hit and run attacks and unleash suicide bombers.
"They are getting ready for a different fight I think. We have a lot tougher days ahead of us than people think. "Al Qaeda on steroids," said Talabany.
"We saw why they were smarter. Al Qaeda never controlled any territory. They will be smarter."
Numerous reports suggesting that Baghdadi had been killed have raised questions about who might replace him as head of a diverse group comprised of Iraqis and other Arabs as well as hardcore foreign fighters.
Iraqi intelligence officers who served under Saddam Hussein have been described as the military strategists instrumental in creating an Islamic State reign of terror.
Talabany said it was hard to know which top Baghdadi aides were alive or dead, but he believes most of the leadership is in Syria, south of Raqqa.
A younger generation of Saddam's former allies were expected to take key positions.
"These are the people in line," he said. "The younger generation is always more dangerous."
Security services face the daunting challenge of breaking up sleeper cells, typically made up of two facilitators and two operators.
"You don't need a lot of guys to set a bomb off. We continue to bust these sleeper cells," said Talabany.
"Everybody we capture was getting ready to set up to carry out attacks in the region."
Talabany left Iraq when he was a 12-year-old boy, at a time when Saddam Hussein was oppressing the Kurds. His relatives were waging a guerrilla campaign from mountain hideouts.
Asked to compare the challenges then compared to those now as Islamic State tries to recover and sectarian tensions threaten Iraq's security, he said:
"We have a lot more freedom now. But the problems are a lot tougher."