Government troops killed nine members of a pro-Islamic State group in the southern Philippines, the military said on Saturday, including two suspects in a deadly blast at a Catholic Mass last month.

Four soldiers were wounded during Thursday and Friday's counter terrorism operation in the Lanao del Sur province, the Armed Forces of the Philippines (AFP) said in a statement, but all are in stable condition.

Those killed were members of Daulah Islamiyah, the AFP said, a pro-Islamic State militant group that took control of the southern Marawi city in 2017 and held it through five months of ground offensives and air strikes by the military.

Among those killed were the two named suspects in the Dec 3 bombing in a university gymnasium in Marawi that killed at least four people and injured 50 others.

"The precision and unwavering dedication exhibited in this operation ... delivered swift and decisive justice for the victims of the despicable attack," Military chief Romeo Brawner said in a statement.

"This operation sets a clear precedent: the AFP will not tolerate those who endanger the lives and well-being of our people," Brawner said.