The administration has denied an entry visa to the widow of slain Chilean president Salvador Allende, saying that her planned address to California church groups on women's and human rights issues would be "prejudicial to U.S. interests."

A State Department spokesman said yesterday that the visa application of Hortensia Allende, 68, had been denied through the U.S. Embassy in Mexico City, where she lives.

The spokesman said the reason for the denial was that Allende is a "highly placed and active member of the World Peace Council, which has a direct political affiliation with the Communist Party of the Soviet Union."

The Reagan administration has criticized the peace council in the past, especially for its opposition to deployment of U.S. intermediate-range nuclear missiles in Europe. Last April the State Department issued a report titled "World Peace Council: Instrument of Soviet Foreign Policy."

Allende, reached in Mexico City, acknowledged that she has attended World Peace Council meetings, but she denied that she was a high official of the organization and said that she was not a member of any political party.

"This is a case of arbitrary action by the Department of State. I don't know why they discriminated against me," she said, noting that members of various communist parties have been allowed to enter the United States in the past. But, she said, "First of all, I am not a member of the Communist Party . . . and I don't think I'm so dangerous at my age."

Allende said she has never been denied a visa since she began traveling around the world to draw attention to human rights violations in Chile after her husband was overthrown in a military coup in 1973. She was last in the United States in 1981, when she attended an anti-apartheid conference at the United Nations.

Rep. Fortney H. (Pete) Stark Jr. (D-Calif.) and other members of that state's congressional delegation yesterday made several unsuccessful attempts to persuade the State Department to approve the application. Allende was invited to the San Francisco area by the Roman Catholic archdiocese there, Stanford University and the Northern California Ecumenical Council, Stark said.

"This is the damndest thing I've ever heard," he said. "Last week we were afraid of Canadians and this week we're afraid of widows . . . . "

Stark's reference was to a Justice Department action against three Canadian films dealing with acid rain and nuclear war. The department, acting under the Foreign Agents Registration Act, required that the films carry disclaimers and that records be kept of the names of groups that have asked to see the films.

"I'm beginning to believe that the Reagan administration thinks that it cannot survive criticism or free discussion of important issues," Stark said. He and Allende said current U.S. relations with the Chilean government of Gen. Augusto Pinochet might have been a factor in the denial of the visa.

The Reagan administration has sought improved relations with Chile, although it appears to have dropped an early effort to certify improvements in Chile's human rights record to Congress in order to reestablish arms sales to the South American country. Allende said that part of her agenda for her U.S. trip was to speak out against Chile's human rights record and the certification.

In explaining the denial of the visa, the State Department spokesman quoted the Immigration and Nationality Act, which states that entry may be denied to "aliens who the consular office or the attorney general knows . . . seek to enter the United States solely, principally or incidentally to engage in activities which would be prejudicial to the public interest, or endanger the welfare, safety or security of the United States."

Allende said she was concerned that the visa denial will be exploited by the Pinochet government and used to discredit her. "In Chile, I am a symbol, as the widow of the last democratically elected president," she said.

Salvador Allende, a Marxist and member of the Socialist Party, was killed on Sept. 11, 1973, the day of the military coup led by Pinochet. The Carter administration made Chile the special focus of President Carter's human rights policy, and relations reached a low point in 1978 when a federal grand jury here returned an indictment against three officials of the Chilean secret police for alleged involvement in the assassination of former Chilean foreign minister Orlando Letelier. Chile has refused to extradite the officials.