A referendum in the southern Philippines Sunday appears virtually certain to reject a major publicly proclaimed policy of the government of President Ferdinand Marcos: local autonomy under Moslem rule for the region.

This rejection, however, would buttress Marcos' personal contention that the commitment to grant autonomy --made grudgingly by the government under pressure of Moslem countries and a four-year rebel war -- is unacceptable to most of the region's 4 million inhabitants.

Christians outnumber Moslems two-to-one in the region, although Moslems predominate in five of its 13 provinces.

Marcos, as a condition toward getting a cease-fire in the rebellion, formally granted autonomy to the region in December but the change has not taken effect and Marcos angered the Moslems by later ordering the referendum. Its purpose, he has made clear, is to demonstrate, especially to the Islamic world, that despite his government's agreement with the rebels, autonomy under Moslem rule is unworkable because it would not be accepted by the population.

In an effort to undercut the significance of the expected defeat, the Moro National Liberation Front, the Moslem rebel force, has called for a boycott of Sunday's voting.

Local Moslem officials. however, are supporting the referendum since they probably would be displaced in the event of a takeover by the younger and more progressive rebels.

A major unknown is whether or not the rebels will try to disrupt the balloting with violence. In four years. the rebellion has resulted in the death of about 4,000 government troops and 10,000 Christian and Moslem civilians.

Although the Tripoli agreement granting the "area of autonomy" was never published locally, it was stated that the zone would have its own security forces and an Islamic court system.

Sessions early this year in the Libyan capital were to have worked out details but the Moslems balked when the Marcos government insisted on the referendum.

The Moro Front and its backers contend that since the bulk of the Christian inhabitants in the south are recent migrants, they should not be given a voice in the affairs of what has been traditionally a Moslem area.

In late March, Libyan leader Muammar quaddafi, chief financial supporter of the rebels, and Marcos' wife Imelda, as special envoy, worked out a compromise. The president was to proclaim the autonomous region and appoint a provisional government from the area that would conduct a referendum to sample views of what sort of administration the people wanted.

Marcos appointed the provisional government but gave it no powers and he ordered the national election commission to conduct the referendum.

Another question, then, is how Libya and other Islamic Conference nations will react to the expected rejection of autonomy in Sunday's vote. Government officials have leaked rumors all week that the Libyan foreign minister would arrive to signify acceptance but there is no sign of him yet.

Since 1974, Islamic foreign ministers have urged the Philippines to negotiate settlement of the war and recently there have been rumored threats of an oil embargo to enforce the point. The ministers meet next month in Tripoli.

Realistically, the settlement sought by the Moro Front would have little chance, since the Christian regional majority would fight rather than be ruled by the Moslem minority.

If the demands were reduced to cover only the five provinces with Moslem majorities, a workable formula might be possible. But these provinces are not contiguous and would be difficult to weld into a single region.