Fugitive Muslim leader Nur Misuari has been charged with rebellion following deadly attacks by hundreds of his armed followers on a southern Philippine city, the justice minister said Wednesday.

A court in the southern city of Zamboanga has issued an arrest warrant for Misuari and three of his commanders for the siege of the city that began on September 9, Justice Secretary Leila de Lima told reporters.

At least 244 people were killed in the three weeks of fighting that followed, with the government alleging that Misuari masterminded the operation even though he was not physically present.

"I'm convinced that we have sufficient and strong evidence this time around to prosecute successfully Nur Misuari," de Lima said.

Hundreds of Moro National Liberation Front (MNLF) fighters occupied parts of Zamboanga for three weeks, taking scores of civilian hostages and battling military and police in a bid to disrupt government peace talks with a rival Muslim rebel group.

The MNLF were eventually driven out and their hostages freed but more than 116,000 people were forced to flee their homes and about 10,000 houses were razed.

The violence was the country's worst since President Benigno Aquino took office in 2010.

Although the government acknowledges Misuari was not among the attackers, it says it has proof he ordered the operation.

His three commanders, Habier Malik, Bas Arki and Assamin Hussin, are accused of leading the attack and are also still at large.

Rebellion carries a maximum penalty of life imprisonment.

Rebellion charges were also laid against 57 other MNLF members who were captured during the fighting that began on September 9.

Asked if police knew where Misuari is hiding, national police spokesman Senior Superintendent Reuben Sindac told AFP he could not reveal such "operational details".

Last week police raided Misuari's Zamboanga home and found explosives and documents.

Misuari and his men were also charged with violations of international humanitarian law over the hostage-taking as well as setting fire to houses, de Lima said.

Misuari's MNLF signed a peace treaty in 1996 that granted limited self-rule to the southern Philippines' 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.

The MNLF believes the deal could leave it sidelined.