The presidential plane is now being used to airlift soldiers wounded in the battles in Marawi City.
On Tuesday night, nine soldiers were flown on board the presidential aircraft from the Philippine Army's Camp Evangelista Station Hospital in Patag, Cagayan de Oro to AFP General Hospital (V. Luna Hospital) in Quezon City.
President Rodrigo Duterte was on hand to oversee the transfer of the soldiers injured in the clashes.
The movements are made to decongest Camp Evangelista Hospital of patients.
Some wounded combatants are already staying at the hospital's hallway.
During the beginning of his term, Duterte had ordered the conversion of the presidential plane into an air ambulance.
He had said he did not need the aircraft.
He explained he was comfortable travelling via commercial flights and small jets.