Abdulham was wanted for a string of attacks, including robbery, but the MILF said the military offensive -- which occurred while Abdulham were holding morning -- was a clear violation of a truce agreement.
"We will file an official complaint with a joint ceasefire monitoring committee," MILF spokesman Von al Haq told AFP.
"It will affect the confidence in the talks, but the incident will not be enough to derail the whole process."
Al Haq said Abdulham was a "field commander" with a following of about 30 fighters.
The group recently announced it had dropped its bid for independence, and said it would settle for the creation of an autonomous 'sub-state' in the south.
MILF leader Murad Ebrahim and Philippine President Benigno Aquino also pledged to fast track peace talks when they held a surprise meeting in Japan early this month.
Those talks are due to resume in Malaysia on August 22.
Copyright AFP (Agence France-Presse), 2011