The State Department acknowledged today that it has denied visas to 348 Japanese peace activists who had planned to attend a U.N. disarmament conference and rally in New York this month.

A department spokesman said the visas were withheld because most were members of a group with indirect communist ties. The visas were denied under the 1952 McCarran-Walter Act.

The unsuccessful visa applicants are members of Gensuikyo. The organization is closely affiliated with the World Peace Council, which in turn has "strong affiliations with the Communist Party of the Soviet Union," the spokesman said. Both Gensuikyo and the World Peace Council are listed as proscribed organizations under the Immigration and Nationality, or McCarran, Act.

Peace groups in New York, who contend that at least 500 persons from a number of countries have been denied entrance visas, say, however, that many persons who had been denied visas identified themselves on their applications as peace activists, not as communists. Applicants who have been turned away include, they say, a former president of Portugal, a former deputy commander for NATO, a British member of Parliament and numbers of other people who have been allowed entry to this country in the past.

"The McCarran Act was written at the height of McCarthyism, and is a misuse of the Democratic process which is supposed to enhance freedom, rather than prohibit it," said Donna Cooper, spokeswoman for the June 12 rally committee. "It's sad if the State Department doesn't see this the conference and rally as something supportive, rather than destructive."

The American Civil Liberties Union said today it plans to file suit against the action, naming Secretary of State Alexander M. Haig Jr. and Attorney General William French Smith as defendants. Smith is reviewing the rejected visa applications as required by law.

New York Civil Liberties Union attorney Steve Shapiro said, "The government's refusal to grant visas has violated the First Amendment rights of the American public to be free to meet and converse and exchange ideas with the foreign representatives of the foreign disarmament movement."

He also said the action of the State Department seemed to hark back to "the worst days of the cold war."

"It shows a lack of self-confidence in the American public and the unthinking and indiscriminatory fear of anything that is remotely connected in any way to communism, which is typically '50s," he said. "There is also something especially upsetting about us interfering this way with the U.N. conference, which was designed to bring people of the world together to deal with disarmament. The government concern should be with disarmament and not the political views of the people coming to discuss it."