The meeting took place on Tuesday on the sidelines of a peace conference in Hiroshima where Aquino and Moro Islamic Liberation Front (MILF) chairman Murad Ebrahim were guests, presidential spokesman Edwin Lacierda said.
A rebel spokesman said the MILF sought the meeting to raise concerns over delays in impleting an accord signed in March, after a draft law that is crucial for a final peace was not passed by Congress this month as planned.
"It is safe to assume that the draft Bangsamoro Basic Law was discussed," Lacierda said.
Muslim rebels have been battling for independence or autonomy in the southern islands of the mainly Catholic Philippines since the 1970s, with the conflict claiming tens of thousands of lives.
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The MILF, with 10,000 armed followers, is the biggest rebel group and its signing of the accord has raised hopes of an enduring peace in the south, despite other breakaway groups still vowing to fight.
A commission composed of rebel and government nominees drafted a "basic law" for the autonomous region, and it was submitted to Aquino in April as part of a timeframe to have Congress pass it by June.
Aquino, however, is still reviewing the planned law. His aides have said this is because he wants to ensure it withstands scrutiny of the legislative body.
MILF deputy chief Ghazali Jaafar told AFP Thursday Murad had sought out the meeting to "express our concerns over the delays", and had been partly appeased by Aquino's response.
He said Aquino must marshall his allies in Congress to pass the law this year. Aquino, in his speech before meeting Murad, highlighted a similar encounter between the two in Japan in 2011 that built momentum in the peace process.
"Trust was established between brothers, and a genuine dialogue was possible," Aquino said.