These were included in a peace plan approved by the national security council, composed of senior cabinet officials and intelligence officials.
The aim is to end decades-long revolts by the separatist Moro Islamic Liberation Front (MILF) and the communist New People's Army (NPA).
An Amnesty and Rehabilitation Commission to be headed by Arroyo's adviser on the peace process will be created to reintegrate former rebels who want to return to the fold, the president's office said in a statement.
The plan also includes "rehabilitation and development of conflict areas", including development to help a backward Muslim autonomous area in the south catch up with the rest of the Philippines.
It will also include an "affirmative action agenda for Muslims", the statement said without giving details.
Affirmative action refers to the policy of giving preferential treatment in hiring and education to marginalized groups to help them reach equal status with mainstream groups.
The peace plan will also include "community-based inter-faith dialogue, healing and reconciliation programs", the statement said.
As part of the peace program, Arroyo called on her advisers to work on local and foreign funding for areas affected by fighting with Muslim and communist guerrillas.
The government has a ceasefire with the nearly-12,000-strong MILF, which has been waging a rebellion in the southern island of Mindanao since 1978. The next round of formal peace talks is expected soon in Malaysia.
The Communist Party of the Philippines (CPP), and its armed component the NPA, is still waging a 35-year Maoist guerrilla campaign to seize power.
The CPP, which has 8,600 guerrillas scattered in the hinterlands, announced last month it was suspending talks with the government because of Manila's alleged failure to persuade Western countries to remove it from their lists of international terrorists.