A long-simmering struggle by Moslem secessionists in the southern Philippines emerged as an election campaign issue today as President Ferdinand Marcos accused the opposition of "treason" over dealings with the Moro National Liberation Front.

The accusation followed reports of a meeting in Madrid recently between Agapito Aquino, the brother-in-law of opposition presidential candidate Corazon Aquino, and Nur Misuari, the exiled head of a front faction seeking a separate Moslem state on the island of Mindanao and other southern Philippine islands.

There were conflicting accounts of the meeting, which took place two weeks ago. The Marcos government charged that Agapito Aquino had signed a "preliminary understanding" with Misuari on recognition of Moslem independence in the southern Philippines should the opposition come to power and an end to the front's 13-year armed struggle.

Marcos promptly termed the purported deal "a sell-out and an act of treason" and government-controlled news media today played up the story, with the government television station showing a map of what the Philippines allegedly would look like under an Aquino government with the southern third of the country lopped off.

Corazon Aquino, who said yesterday that she was unaware of any agreement with Misuari, issued a statement today expressing sympathy for "our Moslem brothers, who were the first to reject the tyranny of Marcos . . . "

She pledged to "respect and substantiate their aspiration for autonomy, to the extent compatible with the territorial integrity of the republic, the democratic rights and liberties of all our citizens and the requirements of national security." She said she hoped to achieve an "honorable peace" in Mindanao if she is elected in the special poll Feb. 7.

In the past several years the Moslem secessionist rebellion has been eclipsed as a security threat on Mindanao by a growing Communist insurgency. But in recent months there have been signs of a resurgence of Moslem rebel activity, with a series of ambushes of government troops and civilians.

As a presidential campaign issue, the secession question has cropped up only days before Corazon Aquino is scheduled to tour Mindanao to stump for votes on the country's second largest island.

Aquino's position on Moslem autonomy seems designed to seek favor with a segment of the population that reportedly is reluctant to vote for her because she is a woman, political observers said. In addition, they said, she may be hoping to weaken the hold of Moslem politicians who support Marcos and whose bailiwicks are notorious for producing large numbers of "ghost voters."

On the other hand, the Marcos government apparently is seeking to raise alarm among the vast majority of Filipinos who are Roman Catholics about the intentions of an Aquino government on the Moslem issue.

"Marcos' new accusation regarding an alleged secessionist deal is, as usual, a lie," Corazon Aquino said. "I pity him."

In a separate statement issued by the Aquino campaign headquarters today, Agapito Aquino acknowledged having held a "dialogue" with Misuari recently, but said it had been distorted by Marcos.

"Nur Misuari and I did not and do not intend to sign any agreement," he said.

He added that while his aim was to restore peace in Mindanao, "peace should never come at the price of the dismemberment of the Philippine republic."

Agapito Aquino said his sister-in-law "had no prior knowledge of my private actions" and that he was not authorized to act on her behalf on such a sensitive subject.

He called on Marcos to implement the Tripoli agreement, an accord signed with the front in 1976 that provided for autonomy in Moslem areas. Some Moslem states and front factions charge that the Marcos government has failed to live up to the agreement.

The Moslem secessionist revolt erupted in the early 1970s and reportedly claimed the lives of 60,000 Filipinos. By the end of the decade the rebellion had largely subsided amid a series of mass surrenders and factional splits. At present there are three main factions, of which Misuari's is reputedly the most militant. The other factions include the Mindanao Islamic Liberation Front headed by Hashim Salamat and the Bangsa Moro Liberation organization of Dimas Pundato.

In other developments today, Cardinal Jaime Sin, the archbishop of Manila, said that senior military officers had promised him they would not stage a coup if Marcos were defeated.

Marcos raised the prospect of such a coup Friday, warning that what he charged was the opposition's cooperation with Communists could result in a "bloodbath" and a military takeover.

U.S. Ambassador Stephen Bosworth told a press club luncheon that Washington was confident it could work with any government produced by credible elections in the Philippines.

But he went on to warn that if the election were marked by fraud and widely perceived as dishonest, "the quality of the relationship" between the United States and the new government inevitably would be harmed.