President Benigno Aquino hopes to secure a final peace settlement before leaving office in mid-2016 to end the rebellion by Muslim groups, which has left 150,000 people dead.
Negotiators met on the outskirts of Malaysia's capital Kuala Lumpur to tackle a "normalisation" deal detailing how the rebels will hand over their weapons and the creation of a security force to police what would be a self-ruled Muslim area.
The deal is the last of four power-sharing accords that must be agreed between the government and the Moro Islamic Liberation Front (MILF) rebels, before a final peace deal can be signed.
"The peace process...Is aimed to really bring about a good foundation for sustainable peace and development in Mindanao (in southern Philippines) and in that sense we consider this a very important development," Ferrer told reporters.
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She added "the bigger challenge of implementation" lay ahead with the target "to substantially complete everything by the end of this administration in 2016".
MILF chief negotiator Mohagher Iqbal said a final peace deal, formally ending the negotiations, was expected to be signed "very soon" to pave the way for peace.
The insurgency, which began in the 1970s, has left parts of the southern Philippines mired in deep poverty and instability.