The aim of the talks is to end a stand-off, in which the Moro National Liberation Front (MNLF) are holding at least 100 people hostage.

Fighting is reported to continue despite a ceasefire agreed between the government and rebels late on Friday.

More than 22 people have died in the violence since Monday.

About 15,000 residents have been displaced by the violence and a curfew is in place.

President Benigno Aquino, who flew to Zamboanga on Friday, earlier issued a warning to the rebels not to harm civilians.

He said government troops had "overwhelming" force and would not hesitate to use it.

Defence Secretary Voltaire Gazmin said the rebels had violated the truce, due to take effect on Friday at midnight.

"Everybody wants peace, to stop this without more bloodshed," Mr Gazmin said.

"But as we speak, there's firing so there's no ceasefire. We agreed that government forces will not fire only if the MNLF will not open fire."

Residents in Zamboanga said gunfire exchanges could be heard throughout the night.

At 2:00 local time, the city government tweeted that the "Police Operations Division says no order of a ceasefire".

On Friday, Vice-President Binay said he had spoken by telephone to MNLF leader Nur Misuari and Mr Gazmin, who both agreed to suspend fighting.

Army spokesman Lt Col Ramon Zagala told reporters at least 52 had been killed, including 43 rebels and four civilians.

Mr Misuari set no conditions in exchange for agreeing to the ceasefire, the vice-president said.

Mr Binay is now travelling to the area to take part in the negotiations.

More than 1,000 troops, backed by police, have been battling to drive MNLF rebels out of the city, who say they are fighting for an independent state.

Officials said the rebels set fire to many homes in the city on Friday as a possible diversionary tactic to try to escape amid shortages of food, supplies and ammunition.

Schools and shops have been closed, with only essential government offices open, according to aid agencies.

The MNLF was founded by Nur Misuari in 1971, with the goal of fighting the Philippine state for an independent Islamic nation. The MNLF then signed a peace agreement with the government in 1996.

However Nur Misuari has complained that his faction has been marginalised in a peace agreement currently being negotiated between the government and another insurgent group, the Moro Islamic Liberation Front.

Last month, he declared an independent Muslim state in the southern Philippines.