Migration and the peace process in the southern Philippines are two of the major issues that will be taken up during Wednesday's meeting between Malaysian Foreign Minister Rais Yatim and Philippine officials, Philippine foreign affairs officials said Tuesday.
The Department of Foreign Affirs (DFA) said the Philippines will seek "improvements in the treatment and working environment of Filipino workers" in Malaysia.
Malaysia is host to around 200,000 Filipino workers.
Manila and Kuala Lumpur nearly severed its diplomatic ties in 2003 after thousands of Filipinos were expelled from Sabah after Malaysia revised its immigration policy against illegal workers.
The Philippine government lodged a diplomatic protest against Malaysia as Filipino deportees accused Malaysian authorities of violating their human rights and subjecting them to torture.
Most of the undocumented Filipinos in Sabah come from far-flung provinces in the war-torn southern Philippines.
Sabah, which is located south of Mindanao, is an island territorially disputed by the Philippines and Malaysia.
Yatim, who arrived Monday night for an official visit, is in Manila as part of the ASEAN's tradition of newly installed Foreign Ministers visiting their counterparts in the region.
Yatim will call on President Gloria Macapagal-Arroyo and is expected to take up the ongoing peace negotiations between the government and the Moro Islamic Liberation Front (MILF).
The 12,000-member MILF, fighting for a Muslim state in southern Philippines since its founding in 1978, signed a transient truce with the government in 2003 but peace talks have been on and off as the two sides cannot agree on the size and wealth of the proposed ancestral homeland for Muslims in Mindanao.
Malaysia, which heads the 70-member International Monitoring Team (IMT) in Mindanao, late last month announced that it will start its phased withdrawal of its peacekeepers due to delays and lack of progress in the peace talks.
Japan and Brunei, who are also members of the IMT that monitors the ceasefire between government troops and the Moro Islamic Liberation Front (MILF), are likely to follow Malaysia's footsteps.
Violence and bloodshed have been significantly reduced during IMT's presence. Church groups and rebel leaders worried that the withdrawal of peacekeepers would induce a new ground of fatal clashes between the government troops and the rebels.
Despite its decision to pull out its monitoring contingent, Malaysia said it will continue to broker the peace talks.
"His visit is expected to enhance our traditional ties with Malaysia - our closest neighbor to the south. It will be an opportunity to explore new areas for cooperation, at the bilateral level and within the context of ASEAN," the DFA said in a statement.
The Philippines and Malaysia established diplomatic relations on May 18, 1964.