But the group has refused to turn over Abdullah Macapaar, also known as Bravo, and Umbra Kato and says it will conduct its own investigations.
Last week, MILF fighters went on a rampage, burning homes and killing residents in two towns after the Supreme Court halted a scheduled signing of a peace deal with the government following opposition from Roman Catholic politicians.
Days later, 31 fighters surrendered to the government saying Bravo ordered the attacks on civilians.
But Bravo denied this and said the men acted independently.
Teodoro said "the MILF central command suffers from serious credibility problems which they must resolve against criminal atrocities committed by their fighters".
Al Jazeera's Marga Ortigas, reporting from the Philippines, explained that the restlessness of its fighters may reflect a power struggle within the MILF.
In an interview given to local media, an MILF ground commander said many in the ranks were growing tired of their leadership's slow progress towards establishing a separate Muslim homeland, making it easy to sympathise with the hardliners.
"Hundreds are ready to join Commander Bravo," he said.
Martitess Vitug, an analyst, told Al Jazeera that "the lines of command have loosened".
"Now that they‘ve been split into small groups and it's a very guerrilla-like operation you need better communication really with better leadership to put them together.
"They can't just blame the government for this they have to do they're own housecleaning or housekeeping, and really show that they're one," he said.
The power struggle within the MILF has led many to question if they government should be talking peace with it at all.
"We are asking the MILF to address that problem otherwise it might only show that they are not very capable in entering into an agreement with us," Hermogenes Esperon, a peace adviser to the government, said.
For the 200,000 displaced residents now living in over-crowded evacuation centres, there are no winners.
The number of casualties continues to rise and those who have lost loved ones in the on-going battle in Mindanao say they no longer know where to turn for peace.