Three of Argentina's most prominent human rights activists have been arrested in Buenos Aires and were being held incommunicado yesterday after a series of raids by plainclothes police officers who also seized numerous documents, according to reliable sources.

Six other persons also were arrested during or after a raid on the office of the Center of Legal and Social Studies, according to human rights workers in London and Washington. Three of the six reportedly were released last night, and they said the other detainees were in good condition.

There was no confirmation of the arrests, which took place Friday night and yesterday, from the Argentine military government.

Jose Federico Westerkamp, a physicist and rights worker, was arrested at the office. A few hours later, police went to the home of Emilio Mignone, Argentina's best-known human rights lawyer and president of the center, arrested him and seized more documents after a 5 1/2-hour search.

Yesterday, after searching his home, police arrested Augusto Comte Macdonell, co-president of the Argentine Permanent Assembly for Human Rights, according to the independent news agency Noticias Argentinas.

The raids were the first crackdown on human rights activity by Argentine authorities since the Reagan administration took office. While human rights was the focus of the Carter administration's uncomfortable relations with Argentina, President Reagan and other officials have made it clear they want to improve ties with the important South American country and will give human rights considerations a lower priority.

The arrests were condemned by human rights organizations including the Service of Peace and Justice headed by Argentina's 1980 Nobel Peace Prize winner, Adolfo Perez Esquivel.

A State Department spokesman said the U.S. Embassy in Buenos Aires would look into the matter, but she declined to disclose any details of the U.S. inquiry.

Sources in Washington said the detainees were being held without specific charges under the state of siege that has been in effect in Argentina since 1974.

A State Department source suggested that there would be little reason to criticize these arrests since they were carried out in connection with a judicial order concerning the seizure of certain documents.

The order was issued by Judge Martin Anzoategui, who also ordered raids on three human rights offices and the seizure of their files just before a visit to Argentina by the Inter-American Human Rights Commission in 1979.

Mignone and Westerkamp, and their center, were better known within Argentina for their human rights activities than was Perez Esquivel before he won the peace prize for similar work. The center was organized in 1979 by a group of lawyers, scientists and technocrats to take quick and effective action in response to political arrests and disappearances. Mignone is also a member of Macdonell's permanent assembly.

Mignone and Westerkamp have children who are among the thousands of Argentines who were arrested or have disappeared since 1974 during formal and informal government campaigns against "subversives."

Also among those arrested in the raid on the center's office was Carmen Lapaco, the organization's treasurer and a member of the Mothers of the Plaza de Mayo, a group of women whose relatives have disappeared.

Others reported arrested at the office included Gabriela Iribarne, an Argentine resident of Canada who apparently had gone there to give an English lesson and who was released last night; lawyer Marcelo Parrili; and doctors Lidia Salazar and Reinaldo Andres Saccone, also freed last night. Boris Pasik, another lawyer and member of the center, was arrested at 4 a.m. yesterday at his home, human rights workers in Washington said.

Amnesty International said in London that Mignone had testified in September before the U.N. Working Group on Disappearances about people abducted by security forces and never seen again. The working group's report was presented last week to the U.N. Commission on Human Rights at its meeting in Geneva.

Mignone's daughter, who worked as a paramedic in a poor neighborhood, was seized by plainclothes police who entered the family apartment by force in 1976, and has never reappeared. The government denies any knowledge of the case, but most observers agree that a majority of the people who have disappeared are dead.

Mignone has lobbied actively seeking condemnation of the Argentine government at the general assembly of Organization of American States in Washington last November.

Eric Stover, human rights coordinator for the Committee on Scientific Freedom and Responsibility of the American Association for the Advancement of Science, said Westerkamp had attended a meeting of North American and Latin American scientists in Toronto in January. The meeting drafted a resolution later adopted by the AAAS Council condemning attacks on "scientific freedom and basic human rights."

Stover said Westerkamp had told reporters in Toronto that the human rights situation had improved in Argentina but that he feared abuses could occur again.

Westerkamp's son, Gustavo, has been in jail without formal charges since 1975. Amnesty International said in its most recent annual report that he had been tortured and kept in an unheated cell during the winter.

Mignone had gone to court twice in January to complain that police had been harassing him and his family.

The Center for Legal and Social Studies issued a report last year saying there was no indication that the Argentine government has any intention of investigating or punishing the abuses committed since the military took power in 1976.