The Iranian revolutionary leader, Ayattollah Ruhollah Khomeini, proclaimed an Islamic republic today without waiting for official results of the two-day national referendum on establishing a new system to replace the deposed monarchy.

"This is the first day of God's government in Iran," said Khomeini, decreeing that it become a national holiday. Joyous gun bursts and chanting of "Allah is great" were heard throughout Tehran far into the night.

The interior minister said more than 98 percent of the electorate voted and 97 percent said yes to the Islamic republic.

This did not seem to take into account results from regions like separatist-inclined Kurdistan, where heavy boycotts of the referendum were reported.

Deputy Prime Minister Amir Entezam said full results would not be known for about five days. Even the proportion of the electorate that voted seemed open to question, since there are no voter registration rolls.

Entezam also predicted that the most likely area for any new separatist rebellion against the Tehran government is Khuzestan, the southwest region around the oil capital of Abadan at the head of the Persian Gulf. It is populated by Arabs, who have been demanding a greater share of income from the rich oil fields concentrated in their area.

"The satanic regime has been cast into the garbage can of history," Khomeini said in his proclamation.

"I will be at your service and at Islam's service in the last few days of my life," said the 78-year-old Khomeini. He called on the government "to reorganize in an Islamic form all the ministries that were set up on Western lines."

It was not clear what was meant by that. Nor is it yet clear precisely what an Islamic republic will be, except that it probably will ban practices frobidden by the Koran, the Moslem holy book, such as drinking alcohol, gambling and immodest dress.

A growing number of people think the final shape of the Islamic republic may have to be settled by a count of guns available to the various factions in the new Iran.

Khomeini said the next step is election of a constituent assembly to approve a new constitution. Spokesman Entezam said a text of the draft constitution will be published next week and that the people will have about a month to discuss it before voting for the assembly's membership.

Asked in an interview why voters were required to do their balloting in the open, where the different colored "yes" or "no" ballots could clearly be seen by partisan observers, Entezam said there had not been enough time to provide booths for the country's 18,000 polling places.

Nobody watched anyone else and it was "a completely free vote," he added.

The head of a four-man delegation of French lawyers invited by the government to observe the voting said: "This is not the way we do things in the West, and it does not meet our criteria of democracy."

Entezam said that he did not yet know whether voting for the constitution assembly would be done in the same public way.

In the debate on the Islamic republic, Prime Minister Mehdi Bazargan made it clear that he opposes a radical rupture of Iranian society. Bazargan told a French interviewer that he had told Kohmeini he is and always has been a gradualist and that, if the ayatollah did not care for that approach, he should replace him.

"The proble," said Bazargan, "is that the populace is still in a state of revolution, while we are a normal government and, in addition, a transitional government. We want people to return to work. Maybe the next, elected, government will be revolutionary."

There is tremendous pressure on the 71-year-old Bazargan to run for president but he keeps insisting that he does not want the job.

"I think he's the only qualified man," said Entezam today.

If Bazargan maintains his refusal, however, some younger men are emerging as likely candidates, with Entezam himself representing the Bazargan-style moderate and Revolutionary Affairs Minister Ibrahim Yazdi the Moslem revolutionary extreme. Somewhere in between is radio-television director Sadegh Ghotbzadeh.

Bazargan has been openly critical of the revolutionary committees with their thousands of well-armed but poorly trained Khomeini supporters providing law and order in much of the country.

There is a race against time to see whether the revolutionary committees will be forged into an effective national military force under Yazdi before the regular armed services are reconstituted.

Bazargan chooses to blame the breakdown in military discipline wholly on Marxists rather than Moslem revolutionaries like Yazdi's followers in the Army's soldiers' committees.

"The Marxists," he said, "want to annihilate the Army under the pretext that is imperialist. We had to fire the whole command of the Army because the soldiers demand it. The extremists are pressing against all the officers. They are doing the same in the police and the gendarmerie so that the government will be 100 percent disarmed."

Bazargan's new defense minister - the old one was relieved apparently for ordering dissolution of revolutionary committees in the Navy - made it clear today that he is on the same wavelength as his predecessor, Adm. Ahmad Madani, and Bazargan.

The new minister, Gen. Taghi Riahi, said it had been a mistake to retire the generals en masse.

"We need a national Army," said Riahi, "but the decision will be made by Kohmeini and the premier. This is a political matter. They must decide. We will take their orders, whatever they decide upon."