Former Muslim guerrillas have taken over governance of a poverty- and conflict-wracked Muslim autonomous region under a peace deal partly aimed at combating Islamic State group-aligned militants in the southern Philippines.

Moro Islamic Liberation Front rebel leader Murad Ebrahim on Tuesday assumed the leadership of an 80-member transition authority dominated by his guerrilla group to govern a five-province region called Bangsamoro. The first large group of about 12,000 combatants is to be demobilized starting this year under the peace deal.

Murad says he and his insurgent group will now wage a new jihad, or holy war, against corruption and other "ills of governance."

Philippine and Western governments and the guerrillas see effective Muslim autonomy as an antidote to nearly half a century of Muslim secessionist violence.