MANILA (Reuters) - Philippine President Rodrigo Duterte held talks with a wanted Muslim rebel leader at the presidential palace on Thursday, immediately after a court suspended a warrant for his arrest, in an effort to bolster his nationwide peace process.

Philippine President Rodrigo Duterte delivers a speech at Philippines Economic Forum in Tokyo, Japan October 26, 2016. REUTERS/Kim Kyung-Hoon/File photo

Nur Misuari had been on the run since September 2013 and charged with leading a bloody rebellion, but Duterte welcomed him and the two discussed how to put an end to nearly five decades of insurgency in the south.

Misuari founded the Moro National Liberation Front in 1969.

He was flown to the presidential palace from his base on Jolo island, home to the al Qaeda-linked Abu Sayyaf militants who run a lucrative kidnapping business and have beheaded foreign and Philippine captives.

Though the MNLF and Abu Sayyaf are not linked, Misuari has recently facilitated with negotiations to secure the release of several hostages.

“I cannot reject his invitation because I respect him,” Misuari said of Duterte.

“He restored my liberty.”

Duterte said he ordered a court to rescind the warrant so he and Misuari could discuss the stalled peace process and what to do about the Abu Sayyaf. Duterte has ordered Abu Sayyaf militants wiped out and has ruled out talks with them.

“We would be able to talk about the problem of our country, the revolution that you have led all these years and finally, understanding on a common ground with government,” Duterte said.

The fight by Muslim militants for self-determination in the predominantly Roman Catholic country has seen more than 120,000 people killed and two million displaced.

The government has signed peace deals with two rival rebel factions but those have yet to be implemented because Congress failed under the previous administration to pass a law creating an autonomous Muslim region in the south.

The ceasefire between the government and the larger faction, the Moro Islamic Liberation Front, has held since 2004. The Misuari-led wing tried in 2013 to seize the mainly Christian city of Zamboanga, triggering a deadly month-long siege.