President Rodrigo Duterte's government is in the process of consolidating present and past peace agreements with all Moro groups in an effort to end a decades-old conflict in which around 100,000 people have died.
Early Thursday, Nur Misuari -- the leader of a faction of the Moro National Liberation Front (MNLF) -- was reported to have traveled from his mountain hideout in the troubled southern province of Sulu to meet with Presidential Peace Adviser Jesus Dureza.
ABS-CBN's DzMM reported that following the meeting, Dureza and Misuari both boarded a private jet to Manila.
Misuari was quoted as thanking Duterte for the lifting of the order, saying it proves he had nothing to do with a September 2013 siege in the southern city of Zamboanga in which around 200 people died.
Last September, Duterte ordered security forces not to arrest the 77-year-old and to temporarily overlook charges of genocide, rebellion and crimes against humanity in an effort to reach a peaceful settlement with Moro groups in Mindanao.
The Misuari faction has accused the previous government of abrogating final 1996 peace agreements with the MNLF when it held negotiations with splinter group the Moro Islamic Liberation Front, which led to the creation of the 2014-sealed Comprehensive Agreement on the Bangsamoro.
The MNLF laid siege to Zamboanga in protest at the framework for the deal with the country's largest Muslim rebel organization.
The 2014 agreement was due to be enforced this year, but was shelved for electioneering for the May 9 presidential vote.