Liberia's military leader, Samuel K. Doe, today was proclaimed the winner of a presidential election that he is widely believed to have lost.

The announcement, made during a one-hour ceremony in a conference center encircled by jubilant armed soldiers, was boycotted by the opposition Liberian Action Party, which informed observers here have said won the election. The party later issued a statement calling the announced results of the Oct. 15 election "a mockery of the law and of the people of Liberia."

U.S. Ambassador Edward Perkins, one of the diplomats invited to the announcement ceremony, was conspicuous in not standing to applaud the results. Perkins refused to comment on the results. The embassy had dispatched nine observer teams to polling places after Congress conditioned the $86 million U.S. aid program here to the holding of fair elections.

In Washington, the State Department issued a statement declaring that while the voting itself "was well conducted . . . we have no information on the vote tallies. The Liberian courts will have to assess charges of misconduct in the tabulation of votes which have been leveled by both the government and the opposition . . . .

"The most recent Foreign Assistance Act linked security assistance to Liberia to the expectation of free and fair elections. We will take these considerations into account as well as economic and development issues in considering future assistance levels."

Monrovia's streets were virtually empty, patrolled by soldiers on foot and in armored cars. The Doe government had declared the day a holiday, and a headline this morning in a government-owned newspaper warned: "No Jubilation Allowed in the Streets."

Dressed in a blue double-breasted suit with a red kerchief in his pocket, Doe sat silently at the head of the conference hall, where members of his government applauded election returns. They were read by Emmett Harmon, whom Doe appointed as chairman of the Special Elections Commission.

Harmon, between announcing that Doe had won 50.9 percent of the total vote and proclaiming him the new civilian president, paused to defend himself and a vote-counting process widely reported to have been fraudulent.

"We feel that as a commission we have truly interpreted the vote of the people of this country and have no remorse of conscience," said Harmon, 72, a lawyer who said his vote-counting procedure "was directed by the hand of God."

The Liberian Action Party won 26.4 percent of the vote, Harmon said, with two smaller parties sharing the rest. It has been two weeks since Liberians turned out in record numbers for what had been billed as the first free, multiparty election in the 138-year history of this nation founded by freed American slaves. Since Oct. 15, there have been almost daily revelations of election-law irregulaties.

Thousands of ballots were burned 10 days ago beside a rural road north of Monrovia. Independent observers confirm opposition party reports that ballot boxes were stuffed with votes for Doe's National Democratic Party.

Harmon, who kept in daily contact with Doe, refused to probe widespread reports of election-day fraud and intimidation of voters by Doe's government. He charged repeatedly, however, that opposition parties had bribed sheriffs and poll workers across the country. The informed observers have dismissed as groundless Harmon's charges, for which he offered no evidence.

Ignoring laws that Doe himself approved for this election, Harmon disqualified an election-night vote count made while observers from the opposition looked on. That count, the observers said, gave the election to the Liberian Action Party's candidate, Jackson F. Doe, who is no relation to the head of state.

To recount the ballots, Harmon created a 50-member committee, comprised mostly of Doe's political backers and 19 members of his Krahn tribe. It counted ballots in secret.

Ever since the then master sergeant Doe seized power here in a 1980 coup, in which president William R. Tolbert Jr. and 13 members of his government were killed, the U.S. government has pressured Doe to hold elections and return Liberia to civilian rule. Traditionally Liberia's closest ally and benefactor, the United States increased aid six-fold during Doe's rule. Per capita U.S. assistance in this nation of 2 million is among the highest in the world.

While employing strong anticommunist rhetoric and professing to be an ardent admirer of President Reagan, Doe had led U.S. diplomats here to believe he would turn power over to a civilian government.

Unemployment here is estimated at about 50 percent and growing. Doe doubled civil service rolls and pay in 1980. His government now is usually four to five months behind in paying salaries.

Diplomats and financial analysts here say Doe's government is plagued by corruption. He has appointed hundreds of members of his Krahn tribe to government-run corporations that now are subsidized. The International Monetary Fund reported this year that $48 million from Liberia's budget was unaccounted for.

During the election campaign, Doe also was pressured by the U.S. government, which threatened to withhold $25 million in aid, to release from jail opposition politicians who had criticized his government.

One of those freed was Ellen Johnson-Sirleaf, a member of the Liberian Action Party who today was declared one of the five opposition winners in the 26-member Senate. In the 64-member House of Representatives, 13 opposition candidates were declared winners.

Johnson-Sirleaf, who had been sentenced to 10 years in prison for sedition for calling leaders of Doe's government "idiots," said today that neither she nor any member of the Liberian Action Party would serve in the new legislature.

"After what has happened here in the past two weeks, both the American people and the Liberian people have been defrauded," she said.