Nine Islamist militants including three suspects in a Catholic mass bombing in the southern Philippines have been killed in a clash with troops, the military said Saturday.

Army soldiers shot it out with about 15 Dawlah Islamiyah suspects hiding out at a mountain farm close to the remote southern municipality of Piagapo on Thursday, the commander of the military unit said.

The firefight left nine of the gunmen dead and four soldiers wounded, including two who were taken to hospital with "serious" wounds, army brigade commander Brigadier-General Yegor Rey Barroquillo told AFP.

He said three of the six suspects in the bombing of a Catholic mass at a school in the southern city of Marawi last month were among those killed in Thursday's fighting.

"Of the nine, three had direct participation in the MSU bombing," Barroquillo said, referring to the 4 December blast at Mindanao State University in Marawi that left four people dead and dozens wounded.

Barroquillo said three other bombing suspects were still on the run including the alleged mastermind, a former student at the university who went by the alias of "Engineer".

Army Scout Rangers, trained in jungle combat, crept up to a cluster of mountain farmhouses where the suspects had sought refuge to evade the post-bombing manhunt.

"Six (gunmen) were able to escape and in our assessment the Engineer was among them," Barroquillo said, adding the farmers had left the area earlier this month after the gunmen arrived.

Militant attacks on buses, Catholic churches and public markets have been a feature of decades-long unrest in the south.

Manila signed a peace pact with the nation's largest rebel group, the Moro Islamic Liberation Front, in 2014, ending their deadly armed rebellion.

But smaller bands of Muslim fighters opposed to the peace deal remain, including militants professing allegiance to the Islamic State group.