The Paraguayan government's release of a U.S.-supplied intelligence document to justify the expulsion of a prominent intellectual here has embarrassed Reagan administration officials seeking to maintain a discreet diplomatic distance from one of Latin America's harshest authoritarian governments.

The on-going controversy began last April with the expulsion of Augusto Roa Bastos, Paraguay's foremost novelist and an expatriate critic of the 28-year-old rule of Gen. Alfredo Stroessner, during a visit here by the writer. He was expelled to Clorinda, Argentina, across the river from Asuncion, and he returned to exile in France.

To support its charge that Roa Bastos had "Bolshevik, ultra-Moscow ideas," the Paraguayan Interior Ministry released a document it said had been supplied by the U.S. Embassy. The one-page photocopy given to newspapers, marked "Secret" in English, includes Roa Bastos among a list of Paraguayans said to have visited Soviet Bloc nations.

U.S. officials have consistently refused comment on the document, although sources here in a position to know have vouched for its authenticity and estimated that it dates from the early 1970s. The official silence has led some Paraguayan opposition leaders to conclude that the Reagan administration may be collaborating with the Stroessner government in the repression of political opponents.

Sources here said that U.S. officials were taken by surprise by the Paraguayan government's action, and U.S. Ambassador Arthur Davis later strongly protested the move in a meeting with Interior Minister Sabino Montanaro. U.S. officials here were not even aware of the existence of the document until it was released, these sources added, nor of when it might have been given to Paraguay. It is from a lengthier text and is undated.

Criticism of the U.S. role was renewed yesterday when the newspaper ABC Color, considered politically independent of the government, published a letter from Roa Bastos to Davis denying two visits to Cuba cited in the document and asking for "the verification and rectification of the erroneous information."

Davis' reply, also printed in the newspaper, said he had "nothing to add" to previous refusals by U.S. officials to comment on the incident.

The controversy over the document came at a time when human rights organizations and political leaders here already were criticizing U.S. officials for shifting from the Carter administration's outspoken pressure on the Paraguayan government to a policy of better ties and "quiet diplomacy" in human rights cases.

The critics here maintain that there has been little change in the level of political repression during the past two years after improvement in conditions during the late 1970s.

"It is clear to us that the Carter policy of confronting the dictatorship got far more results than that of Reagan," said Juan Benitiz Florintin, the president of the opposition Authentic Radical Liberal Party. "We think Reagan is comfortable with Stroessner because he is an anticommunist, and that is all that Reagan focuses on."

By both diplomatic and rights groups' accounts, Paraguay remains a center of political repression in South America. A poor, landlocked nation the size of California, Paraguay has never known democracy. Fifty-six political prisoners are currently in Paraguayan jails, and hundreds more were held for brief periods during the last year, according to human rights groups here. Almost all of those arrested were beaten and tortured, rights organizations and diplomats charge.

U.S. officials here acknowledge that improvement in human rights has been stalled in the past several years and that their standing has declined among opponents of the government. They say, however, they have continued to work actively in support of political prisoners.

Officials here also point out that the Reagan administration has not restored the once close military and political ties with Paraguay, to the evident disappointment of Stroessner and his lieutenants.

Administration officials suspended a largely symbolic policy of voting against aid and loans to Paraguay in international organizations, and last year appropriated $50,000 in training funds for the military--far below the $800,000 in annual aid and equipment Paraguay received prior to the Carter administration's suspension of military cooperation.

U.S. officials have sought to limit the damage of the expulsion by stressing to newspapers and opposition leaders here that the writer is welcome in the United States and is not considered a communist.

But political leaders here, who say Roa Bastos has never been affiliated with a political party, remain skeptical. "I don't understand why nothing has been said when an obvious injustice was committed on the basis of information that was wrong," said Rafaela Guanes de Laino, the wife of the recently expelled leader of the Paraguayan opposition, Domingo Laino. "He who is silent accepts."