Philippine President Benigno Aquino and the head of the country's main Muslim rebel group agreed during a secret meeting in Japan to speed up peace talks, the government said Friday.

"Both agreed to fast track the negotiations," a Philippine government statement said after Aquino met Moro Islamic Liberation Front (MILF) chairman Murad Ebrahim on Thursday near Tokyo's Narita airport.

"Both agreed that the implementation of any agreement should happen within the current administration," it added, referring to Aquino's six-year term that ends in mid-2016.

MILF vice-chairman Ghazali Jaafar also told AFP by telephone from the southern Philippines that the Japan meeting had been a success.

"It's a fruitful meeting. The government is serious in looking for (a) genuine solution to the problem," said Jaafar, who did not travel with Ebrahim.

The 12,000-strong MILF has been waging an insurgency for more than three decades to carve out a separate Muslim state in the mostly Catholic country's southern island of Mindanao.

The rebellion has killed over 150,000 people and stunted economic growth in the mineral rich but impoverished southern region.

Aquino's predecessor, Gloria Arroyo, failed to sign a peace deal with the MILF during the nearly ten years she was in power.

Large scale fighting erupted in 2008 when rogue MILF commanders launched attacks in response to the Supreme Court outlawing a proposed peace deal that would have given them control over vast tracts of land.

More than 750,000 people were displaced at the height of the fighting, triggering a humanitarian crisis.

About 400 civilians and fighters from both sides were also killed.

After Aquino came to power last year, peace talks resumed between the two sides in Malaysia, with the last round held in June.

The government said Friday that the Japan meeting was the first time a Philippine president had held face-to-face talks with the MILF chairman in 14 years of on-and-off peace negotiations.

The official negotiating panels of the two sides are now expected to head back to Malaysia to continue the talks in the middle of this month, both parties said.

The MILF broke away in 1978 from the Moro National Liberation Front, which launched a bloody separatist uprising in Mindanao in 1971 before signing a peace treaty with the Philippine government in 1996.

The treaty created a limited self-rule area called the Autonomous Region in Muslim Mindanao that has so far failed to uplift the condition of Filipino Muslims, who remain among the country's poorest.

The MILF is the largest rebel group in Mindanao, but the area is also home to a small band of Al-Qaeda-linked Islamic militants, as well as other armed groups who conduct kidnappings and extortions to raise money.