The institute said the quake, which struck at 4:41 a.m. local time (2041 GMT Wednesday), hit at a depth of 470 km, about 17 km northeast of Palimbang town.
The institute said the tremor, which was tectonic in origin, was also felt in Cagayan de Oro City.
There was no reported casualties or damage.
The institute said aftershocks are expected.
The U.S. Geological Survey said the quake has a magnitude of 5.5.