"The MILF is not selective of any leadership in Malacañang," Mohaqer Iqbal, MILF chief peace negotiator, said in a statement posted at the rebel website at luwaran.com.
"The MILF is dealing with the Philippine government and I presuppose that whoever is sitting as president, the government is morally and legally obliged to respect and implement whatever political agreement both parties have forged."
Iqbal said the government and the MILF peace panels are now in Malaysia to resume the stalled peace talks.
Following a successful general assembly held in Darapanan, Maguindanao last month, which was attended by some one million sympathizers, the government and MILF peace panels are optimistic that a final peace agreement could be drawn up soon, he added.
Earlier, MILF spokesman Eid Kabalu said the rebels would not take part in any plot to destabilize the government and oust President Arroyo.
"We are maintaining here our non-interference policy with matters internal to the government," he said.
"We will not be siding with anyone. We will maintain our neutrality, consistent with the policy of the MILF of non-interference in such affairs."