Police lodged the complaint against Misuari and against his followers, who fought street battles with police and troops in Zamboanga city last month in which more than 200 people died, said senior police investigator Senior Superintendent Edgar Danao.
"We have gathered affidavits linking Misuari to the said attack," Danao told reporters Thursday, a day after the complaint was filed with the state prosecutor's office.
Misuari is accused of sending his armed Moro National Liberation Front (MNLF) followers to Zamboanga on September 9 to try to block a proposed peace deal between the government and a rival Muslim rebel group.
The incursion sparked three weeks of street battles with elite military forces that forced more than 100,000 people to flee their homes.
The government accused the gunmen of taking civilian hostages and setting fire to more than 10,000 homes.
It declared the rebel action crushed on Saturday with the release of the last of 195 hostages.
Apart from at least 189 guerrillas killed, the campaign also left at least 23 soldiers and police and 12 civilians dead.
Misuari, 71, is believed by police to have gone into hiding.
Police have so far filed complaints for rebellion and other criminal cases against 224 MNLF leaders and followers, most of them now detained, said regional police spokesman Chief Inspector Ariel Huesca.
State prosecutors will evaluate the evidence submitted by police, then decide whether to bring charges in court. Rebellion is punishable by life imprisonment.
Muslim rebels have been fighting since the 1970s for an independent or autonomous homeland in the south of the mainly Catholic Philippines. An estimated 150,000 people have died in the conflict.
The MNLF signed a peace treaty in 1996 that granted limited self-rule to the south's Muslim minority.
However, the group opposes a planned final peace deal between the government and the remaining major Muslim rebel group, the 12,000-strong Moro Islamic Liberation Front.
Misuari apparently fears the proposed peace deal would sideline him and his group.
