President Rodrigo Duterte declared Marawi City liberated six days ago, even though battles were still ongoing.
The news comes as a surprise to multiple Filipino officials, who say they have no knowledge of such an operation.
The Philippines military said child soldiers are among the fighters left in the embattled city.
The militants have been holed up in the city since May 23, trapping hundreds of civilians.
"I can end this war in 24 hours. All I have to do is to bomb the whole place," Philippines President Rodrigo Duterte said.
Attached to one of the bodies was a sign that said "Munafik", meaning "traitor."
Militants took a local priest and more than a dozen churchgoers and staff hostage.