The forces are providing technical help and are not fighting, it said.
President Rodrigo Duterte had earlier threatened to throw out US troops amid strained relations since taking office.
Militants have been under siege since rampaging through the southern city on 23 May. The latest fighting has claimed the lives of 13 Philippine marines.
Hundreds of militants, who have been flying the black flag of so-called Islamic State and are led by the self-styled IS emir of the southern Philippines, Isnilon Hapilon, and the Maute brothers Omar and Abdullah, are still holed up in the city.
The latest casualties bring the number of Philippine troops killed in the fighting to 58.
At least 138 militants and 20 civilians have also been killed, the government says.