Philippines President Ferdinand Marcos, seeking an electoral mandate to extend his 16-year rule, swept to an easy victory today in an election boycotted by most of the country's opposition groups.

The widely expected win gave the 63-year-old Marcos a six-year term under a newly amended constitution that allows him unlimited reelection to a strong French-style presidency.

The election also marked the Philippines' formal return to elective government following more than eight years of martial law.

Marcos said in his home town of Batac, in the nothern Philippines, that one of his first tasks will be "to bring about a . . . reconciliation" with his political opponents.

In remakrs to reporters, he said, "You have only two alternatives here. Either you do it with a soft hand or you do it with a tough hand. I intend to do it softly."

Although the voting itself was generally peaceful, 13 persons were reported killed today in two provincial clashes between government troops and suspected communist guerrillas, and opposition groups accused the government of arresting 45 boycott advocates.

The opposition groups called the boycott to protest alleged irregularities during an April 7 plebiscite on the constitutional amendment, which passed by a hugh margin.

According to the Philippines Commission on Elections, today's early returns showed Marcos winning 86 percent of the vote. His nearest rival, Nacionalista Party candidate Gen. Alejo Santos, was receiving 10 percent, and a candidate favoring American statehood for the Philippines, Bartolome Cabangbang, was taking 4 percent, the commission said.

Based on these returns, Philippines television stations late tonight declared Marcos the overwhelming winner of the country's first election in a dozen years. However, opposition candidates and boycott leaders immediately called the election a fraud and charged that voting irregularities padded Marcos' victory.

The government and its leading opponents also differed on the effectiveness of the boycott. The commission on elections claimed a turnout averaging 85 percent nationwide and said that the boycott had flopped. An umbrella group of oppositon parties asserted, however, that its own survey of metropolitan Manila showed only 58.6 percent of registered voters went to the polls today.

An independent survey of 14 randomly selected precincts in different parts of the capital showed a turnout of 65 percent. Of the ballots cast, 78 percent were for Marcos, 10 percent for Santos and 4 percent for Cabangbang. pNearly 8 percent were blank, marked "boycott" or defaced. When the number of these ballots was subtracted from the turnout, the percentage of registered voters actually participating in the election dropped to 60 percent.

One of the boycott leaders, former newspaper publisher Joaquin Roces, declared the action a "success" and said the turnout would have been even smaller if the government had not "created a lot of fear" by threatening to prosecute nonvoters. A 1978 decree by Marcos' martial-law administration made failure to vote a crime punishable by up to six months in prison and future ineligibility for public office.

"I feel we have won as far as the boycott is concerned," Roces said. He accused Marcos of padding his winning percentage with various irregularities including the use of "flying voters" transported from one polling station to another.

Roces said the opposition grouping had not yet met to consider its strategy now that Marcos has won a new presidential term. But he said, "We will continue to try to change the situation."

In an apparent effort to ensure an unblemished electoral mandate after his years of martial-law rule, Marcos during the past few weeks had repeatedly urged the Philippines' 25.8 million voters to participate in today's election. uTo put teeth into its appeal, the government also began court proceedings against some Filipinos, including a major opposition figure, who failed to vote in the April 7 plebiscite. A few days before the election, however, the government offered an amnesty to the April nonvoters, provided they participated in the presidential election.

The boycott issue also triggered a conflict between the government and the leadership of the influential Roman Catholic church over whether failure to vote consititues a "mortal sin." Reacting to a statement by Marcos quoting Pope Pius XII as saying that not voting was "a grave sin, a mortal offense," the archbishop of Manila, Cardinal Jaime Sin, argued that the 1948 quote had been taken out of context and that abstention in this election was a matter of conscience.

The dispute has further worsened relations between Marcos and the church, which generally seems more sympathetic to the opposition.

After he had cast his ballot in his home province of Ilocos Norte, where in some areas he received 100 percent of the vote, Marcos indicated to reporters that he might consider allowing exiled Filipino opposition leaders to return home. He also again raised the possibility of an amnesty for those who did not vote in the April plebiscite.

Besides changing the Philippines' presidential system from an American-style, four year presidency limited to two terms, the plebiscite also allowed Marcos immunity from suit. Under the new constitutional amendments, the president will preside over a parliamentary sytem that includes a prime minister and a unicameral legislature.