In an election marred by voter intimidation and flagrant irregularities at some polling places, Liberians turned out today in large numbers to select a civilian president for this West African nation.

At one unauthorized polling place set up today at Army barracks in downtown Monrovia, voters were free to cast as many ballots as they wanted. There were no registration lists. Some election workers, handing out ballots from briefcases, made no attempt to verify if the recipient previously had voted.

This came under the watchful eyes of khaki-clad soldiers and observers wearing campaign T-shirts and hats bearing the initials of the political party headed by Samuel K. Doe, who for five years has been the military leader of Liberia and is one of four candidates for president.

Observers from the other three parties were not present, as is required by election regulations.

At two rural polling places north of this port capital, voters in the town of Kakata were not allowed to mark their ballots privately, as required by election regulations. In one bamboo school house there, voters were required to call out their choice for president in a room filled with government officials.

"These are clear violations," said Ellen Johnson-Sirleaf, a senatorial candidate for the opposition Liberian Action Party.

"It was very clear in the election rules that nobody was to be in the presence of the voter. The ballots at the Army barracks should be declared invalid," she added.

Despite these irregularities, which were witnessed by this reporter, observers from opposition parties reported a large turnout across Liberia and said a majority of polling places were properly supervised.

The U.S. government, long a major benefactor of this impoverished country founded in 1847 by freed American slaves, is watching today's election with particular interest.

Ever since former Master Sgt. Doe and 12 of his colleagues overthrew the government, killing the president and more than two dozen other officials, the United States has been lobbying to return Liberia to elected civilian government.

To that end, it has courted the former noncommissioned officer who has promoted himself to general.

In long one-on-one sessions, an American ambassador here for years tutored Doe in the art of statecraft. Doe was invited to the White House to meet President Reagan. To improve his English, Doe studied videotapes of Reagan's speeches.

Washington increased aid six-fold to Liberia, making this country of just 2 million people one of the highest per-capita recipients of U.S. assistance. Assistance, which averaged $15 million a year before Doe, is $86 million this year.

For his part, Doe espoused strong anticommunist policies and rhetoric and said he was an admirer of all things American. According to diplomats, he watched Reagan's speeches via a satellite dish installed on the lawn of his mansion.

The result of the American largesse was to come with today's election of a civilian leader.

For more than two years, the U.S. State Department believed that Doe would not be a participant.

Early in his tenure as head of state, Doe had led American diplomats here to believe he would turn power over to a civilian government and return voluntarily to his Army barracks.

But to the chagrin of the Americans, Doe last year declared that he would run for the presidency. Since then, he has presided over a strong-arm campaign.

His government has banned the candidacy of his two strongest challengers, jailed and allegedly flogged dozens of political opponents, shut down newspapers and invoked a decree that allows the arrest of anyone who spreads "rumors, lies and disinformation."

According to documents here, civil servants have been ordered to campaign in support of Doe's party, the National Democratic Party of Liberia. They also have been ordered to give contributions to that party. A "task force" of burly young party militants, including paid recruits from neighboring Sierra Leone, has beaten and intimidated opposition political workers across the country.

Members of the task force presided, along with soldiers, over the unauthorized voting at the Army barracks in Monrovia. The Special Elections Commission of Liberia, in its published list of official polling locations, did not mention that voting would occur at the barracks.

Last week Doe warned on Liberian state radio that if he did not win the election, the Army would revolt within two weeks. The results of today's voting are expected to take two weeks to be counted.

The three civilian presidential candidates who have been permitted to mount campaigns say they are far more worried about intimidation at the polls and election fraud after the polls close than they are about Doe's popularity with voters.

Political observers and diplomats here say that the opposition Liberation Action Party, whose candidate is Jackson F. Doe (no relation to the head of state), has a strong support among Liberia's 751,000 voters.

There are no nationwide polls in this rugged and undeveloped country where large numbers of voters live two days' travel from a paved road. But an official in Doe's Ministry of Information conceded that the head of state probably would lose in a "free and fair election."

Samuel K. Doe, who was thought to be 33 but allegedly changed his age to 35 so he would be eligible under the constitution to run for the presidency, has conducted an election campaign that appeared as much designed to alienate voters as win their confidence.

In July, he announced a 25 percent salary surtax, with the proceeds to go for a new studio for the national radio station. Market women, an important political and economic force in Liberia, have been forced to join Doe's party or close their shops.

Even the Army, Doe's base of power, has been irritated by a mandatory $5-a-month tax that went to support Doe's campaign.

A long series of government arrests, disappearances and beatings has brought expressions of U.S. concern and cast doubt on Doe's willingness to leave office if he does lose.

Cherbutue Quayeson, an opposition candidate for the new civilian legislature, says he was stripped of his clothing in an Army barracks Sept. 30 and given 50 lashes with a cowhide whip.

The 40-year-old high school principal and member of the opposition Liberian Action Party said last week that his crime was to march with other opposition candidates in Zwedru, a town in Doe's home county, Grand Gedeh.

Quayeson, whose back is badly scarred, said soldiers broke up the march, and searched house-to-house in Zwedru for politicians who had fled. The government has said the march was dispersed because it was illegal and caused a disturbance. Quayeson said he had received permission from the county superintendent for the march and that it was peaceful.

"I was hiding in a friend's house behind a locked door when they burst the locks," he said. "I was told to lie on the ground. A solider stood on my head. The pain was unbearable."

After being flogged along with 14 other members of his party, including four women, Quayson said, he was jailed until last week.

The most notable jailing of an opposition politician occurred in July when senate candidate Johnson-Sirleaf was charged with sedition for referring, in a speech in Philadelphia, to the "many idiots in whose hands our nation's fate and progress have been placed."

Johnson-Sirleaf, a former World Bank economist and one-time finance minister in Liberia, was later sentenced to 10 years in prison.

Under pressure from the U.S. government and several African leaders, Doe two weeks ago released Johnson-Sirleaf, along with several other political opponents.

Within 24 hours of their release, the State Department released $25 million in economic aid that had been withheld because of concern over human rights violations and economic mismanagement in Liberia.

Congressional language in the 1986 foreign aid bill threatens to cut all U.S. aid to Liberia if today's election is not judged to be "free and fair." That assessment will be made by American diplomats here, who sent nine teams of observers.

Johnson-Sirleaf said today the key to the fairness of the election is what happens to ballots once polls close.

"If they count the ballots on the spot, with our observers watching, then our fears are minimized," she said. But, if ballots are not counted before being returned to election headquarters in Monrovia, she said "there is no way we can control the fraud."