The U.S. government has granted entry visas to more than 5,000 Iranians who fled feared religious presecution by the regime of Ayatollah Ruhollah Khomeini in the four months since the seizure of the American hostages in Tehran.

The influx of religious minorities -- mostly Jews and Bahais -- is part of a general exodus of such groups from Iran in the year since the fall of shah Mohammad Reza Pahlavi. It is estimated, for instance, that half the 80,000 Jews in Iran have left the country since Kohmeini took power.

Strikingly, the stream of Iranians to the United States has come at a time that the Carter administration was cracking down on students from Iran who were in the country illegally.

Statistics from the Immigration and Naturalization Service show that in the past four years, 11,079 Iranians, including 2,306 students, have entered the United States. In the same period, 12,694 Iranians, including 2,946 students, have left the country.

Administration officials stressed yesterday that there is nothing consistent in continuing to allow Iranians with legal visas to enter the country during the hostage crisis. "We are a nation of laws," a State Department spokesman said.

But some of the same officials acknowledge they are reluctant to talk about the quiet policy of giving "special consideration" to the religious minorities from Iran. "It's an incredibly ticklish situation," said one congressional expert on the subject.

"Eventually it will become clear that the Jews and other minorities in Iran will be what we consider refugees," said one Justice Department official familiar with the situation. But we don't want to do anything now to polarize relations with Khomeini."

State and immigration service officials said they could not estimate how many Iranian nationals have left their homeland since the Islamic revolution, or how many are now waiting in some European capital trying to gain entry to the United States or some other country.

Arthur Pruzan, an official of the Hebrew Immigrant Aid Society (HIAS) in New York, said yesterday that his group estimated that 40,000 Iranian Jews have fled since the Khomeini takeover because of the ayatollah's anti-Zionist statements. About 25,000 have emigrated to Israel and 10,000 to 15,000 to the United States he said.

"After the hostages were taken, the numbers of people leaving Iran slowed down," Pruzan said. "That's because things got tougher for entering the U.S."

State Department officials said that consular officers in Europe are instructed to check visa applicants closely because of the hostage crisis. And Iranians who enter the United States automatically are pulled aside now for "secondary inspections."

But a State Department spokesman said one consular official told him, "We're flipping over backwards" for the Iranian religious minorities.

In fact, one State official said, it is estimated that half of all the visas issued to Iranians since the Khomeini government took over have gone to religious minorities.

There is some consideration now, some officials noted yesterday, to allowing some of those Iranians still wishing to enter the United States to do so as "parolees," to get around the sensitive issue of calling them refugees.

The latest collapse in negotiations for release of the approximately 50 American hostages in Tehran triggered a barrage of queries about the status of Iranian students and the highly-publicized administration promise to oust most Iranian diplomats.

Only 700 of an estimated 10,000 Iranian students who refused to report as ordered to immigration officers for a visa check late last year have been found so far this year, officials said. And more than half the 226 Iranian diplomats who were supposed to leave the country couldn't be located either, they added.

To date, more than 800 students who were found to be deportable because of flaws in their visas have applied for political asylum in this country rather than return to Iran, immigration officials said.

During the original check on Iranian students, 6,900 of the 56,700 who reported were found deportable. More than 1,000 of those left the United States voluntarily, 5,500 have deportation hearings scheduled and about 60 have been deported, according to INS records.