UNITED NATIONS, OCT. 2 -- Iran has been secretly permitting thousands of its Jewish citizens to leave the country via Pakistan and then Austria and emigrate to the United States and Israel, Austria's foreign minister said today.

Alois Mock, who also heads the conservative People's Party in the Austrian government coalition told reporters at a U.N. luncheon that 5,100 Iranian Jews had come through Austria since 1983.

The flow has increased sharply, to 1,483, in the first eight months of this year, he said.

Israeli officials said last year the number of Jews in Iran had dropped to 30,000 from an estimated 80,000 who lived there before the 1979 Islamic revolution.

Mock said the immigrants cross the Iranian border in buses, without any opposition from local authorities on either side. They are flown to Vienna, and then choose their final destination.

Israeli officials here confirmed Mock's basic information about the exodus of Iranian Jews. The fate of Jews in Iran has been an important consideration in Israeli policy toward that country, and Israel has acknowledged selling arms to Iran.

But the officials flatly denied reports that they said had been circulating in London that the immigration was linked to continued shipments of Israeli arms to Tehran.

Austrian officials confirmed that Mock was making this information public on the eve of Yom Kippur, the most important Jewish holiday, to demonstrate to people in the United States and the West his government's positive attitude toward the human rights of Jews and others. Austrian President Kurt Waldheim has been accused of participating in or having knowledge of Nazi atrocities in Yugoslavia and Greece during World War II.

Mock also noted at the lunch that the flow of Soviet Jews through Austria had increased sharply this year, apparently as part of Moscow's policy of glasnost, or openness. He said that 901 Soviet Jews had come through Austria in the first eight months of 1986, and the figure had jumped to 5,003 for a same period this year.

Mock also told reporters that he had met with three groups of American Jewish leaders while in New York. While some raised the allegations about Waldheim's activities during World War II, "I was very pleased by the fairness of the discussion, even with those who disagreed with me," he said.

Mock denied, however, that there had been any quid pro quo for Iran from Austria for allowing the Jews to leave. He cited an Austrian law barring arms sales to any war belligerents and noted that only two shipments of Austrian arms were known to have reached Iran illegally.

One shipload, he said, may have gone through Libya in 1985 or 1986. And 110 artillery pieces went to Iran through Brazil. This was discovered, Mock said, "when our people were told by the Brazilian Army that the arms they had ordered had not arrived."

Austria has had a national policy of facilitating the flow of refugees from East Europe and other parts of the world since 1945. Mock noted that more than 2 million refugees or immigrants had passed through Austria since then, includ-"I was very pleased by the fairness of the discussion."

-- Austrian Foreign Minister Alois Mock

ing 272,000 Soviet Jews and 115,000 Jews from other countries of Eastern Europe.

Austria has faced difficulties in its relations with Israel and the United States since the revelations in early 1986 of Waldheim's World War II record. Mock's trip to New York and Washington was designed in part to ease these strains. He said he has no official contacts with the Israelis here but "we will see what will happen in the next month."

In Washington, Charles Nasem of the U.S.-Pakistani Alliance said he thought about 500 Jews had left Iran via Pakistan during the past year in about 10 or 15 convoys. Nasem said the Pakistani government of Gen. Zia ul-Haq gave the Jews "no objection certificates," permitting them to pass through the country.

Nasem, whose organization promotes better U.S.-Pakistani relations, said the Jewish immigration through Pakistan was "a political compromise with the Zia government to let the Jews go through under the banner of the U.S.-Pakistan Alliance and the Iranian Jewish Refugee Association."