Duterte in July shelved negotiations to end one of the world's longest insurgencies after the rebels refused to discuss a ceasefire and continued deadly attacks.
In the latest flare-up, an army unit clashed with a small force of New People's Army (NPA) guerrillas near the town of Carranglan, about 150 kilometres north of Manila, early today, the provincial police chief said.
"The residents reported the presence of armed men in their area. The soldiers went to the area and that is the start of the firefight," Senior Superintendent Antonio Yarra told reporters.
It was unclear why the military casualty figure was so low compared to the insurgents.
Troops recovered the bodies of the nine guerrillas and their rifles, said Lieutenant-Colonel Isagani Nato, military spokesperson for the northern Philippines.
The NPA, now estimated by the military to number around 3,800 fighters, has waged a low-level guerrilla war that has left 30,000 people dead since 1969, according to government estimates.