Philippine government and Muslim rebel negotiators will meet in Kuala Lumpur on Thursday for the first time since a wave of bloody clashes erupted in the troubled south, a rebel official said.

The informal talks in the Malaysian capital will address an on-off peace process and the tensions that surged over two weeks of bloody fighting in October, which left as many as 40 soldiers, police and civilians dead.

"The talks are more important now because there are many issues to discuss such as what happened (in October)," Ghadzali Jaafar, vice-chairman of the 12,000-strong Moro Islamic Liberation Front (MILF), said on Wednesday.

But he said the new talks were scheduled before the outbreak of fighting between government forces and MILF-linked gunmen last month, and dismissed the clashes as a "minor issue".

In two different areas in the Philippines' Muslim-dominated south, a pursuit of wanted outlaws turned into pitched battles with MILF-linked fighters.

The MILF later disowned some of the gunmen involved but also blamed the military for intruding into its territory.

Since then, government officials have warned the MILF that it may come under attack if it continues to shelter the "lawless elements".

"If the military fires at the MILF, the MILF will fire back. We have not done any provocation. We just want everything to pass through the (peace) process," Jaafar told AFP.

Government negotiators could not be reached for comment.

The two sides are ostensibly meant to be observing a ceasefire. Long-running negotiations stalled after the MILF snubbed Manila's "roadmap" for peace in August.

The Muslim rebels, who now want autonomy after long fighting for a separate state in the mainly Christian Philippines, initially said they would not resume talks unless the government changed its proposal.

But Jaafar said that Malaysia's government, which has been facilitating the talks, had persuaded both sides to try to air their differences.