A pastor has been taken hostage and several Christians are among the many injured in an attack by a rebel group in the Philippines.

The Moro National Liberation Front (MNLF) is suspected of carrying out the attack on September 9 in Zamboanga, Mindanao province, which left at least six dead.

At least 20 people have been taken hostage, including a pastor, whose name is being withheld for security reasons. More than 800 have fled their homes, including from the busy Rio Hondo area. A local church has been tending to casualties.

The city has been placed on Red Alert with schools cancelled and businesses closed. Officials say the rebel group has been using hostages as human shields as they march towards the City Hall.

The MNLF has been seeking independence for decades, hoping to create an independent Islamic state. A ceasefire was agreed in 1996, but some of the group's affiliates remain active.

Asamin Hussin, National Security Commander for the MNLF, told AP news agency that they wanted independence.

"We want to establish our own Bangsamoro government, not an autonomous government but we want an independent Mindanao as Bangsamoro nation," he said. Bangsamoro refers to Muslim people in southern Philippines.