Ayatollah Ruhollah Khomeini today overruled his revolutionary government and barred any negotiations with two envoys from President Carter for the release of at least 60 Americans being held hostage in the U.S. Embassy here.

The Foreign Ministry confirmed that the visit of former attorney general Ramsey Clark and Senate staff member William G. Miller had been arranged with the full knowledge and approval of the Revolutionary council. Khomeini appointed the council as his new government yesterday after the resignation of prime minister Mehdi Bazargan.

Clark left Andrew Air Force Base Tuesday night accompanied by Miller, a senior staff member of the Senate Intelligence Committee. They had been expected to arrive in Tehran in the early hours of Thursday morning and to proceed swiftly to the holy city of Qom with a message for Khomeini from Carter.

But in a statement rleased only hours before Clark was due to land in Tehran, the 79-year-old ayatollah said that he would not meet the mission and forbade all other responsible officials from having contact with it.

"The U.S. government has announced its opposition to Iran by giving shelter to the ex-shah, and it has been revealed that the American Embassy in Tehran has been a place of espionage against us," the ayatollah declared. "It is not possible for the special representatives to meet with me.

"The Revolutionary Council should not meet with them at all, and no responsible official is permitted to meet them," Khomeini continued.

In a final comment that leaves Washington little room for maneuver, Khomeini said, "Once the United States has delivered the deposed shah, the number one enemy of the nation, and once it has discontinued espionage against our movement, the door would then be opened for negotiation on some relations in the interest of the nation."

No further news of the hostages has been provided by the students occupying the U.S. Embassy. Today they appeared openly carrying weapons for the first time.

Bruce Laingen, the highest ranking American here, has been granted refuge inside the Foreign Ministry, the official Iranian news agency Pars said today. Laingen, who is U.S. charge d'affaires, was not in the embassy at the time it was seized by the students.

The students declined to hold the daily press conference that has taken place since they occupied the embassy on Sunday and there has been no indication of when, if at all, the press will be able to meet the hostages as previously promised.

In the meantime, Khomeini aides and the national Iranian Oil Company adamantly denied reports that they had suspended oil supplies to the United States or that there had been any disruption of production and export operations.

"Everything is normal, we have no problems, there is no shortage of oil and there is no queue of tankers," said one senior director.

U.S. officials and international oil company executives said, however, that oil deliveries had been cut briefly Tuesday.

Acting Oil Minister Ali Akhbar Moinfar said today the production was continuing at about the programed rate of 4 million barrels a day. Moinfar recently warned that Iran would cut supplies to the United States if so ordered by Khomeini. But he said no such order had been received and aides to Khomeini in Qom today confirmed that no such order had been given.

But members of the U.S. business community are continuing to leave Iran following the advice of the State Department that they could no longer count on normal consular support and protection.

Many of those remaining have stayed away from their offices and some have changed accommodations reflecting concern at rumors that Iranian students would step up the psychological pressure on the United States by seizing more hostages.

Three U.S. citizens were detained today by revolutionary militia at Tehran's International Airport shortly before they were due to board a Swiss Air jet but were released in time to catch a later flight out.

Tehran radio early today broadcast a communique from the students occupying the embassy which called on the public not to harass foreign nationals, describing such action as counterrevolutionary.

The students, who yesterday threatened to kill the hostages if the United States attempted any military or covert action to obtain their release, advised "Do not with irresponsible act prepare the ground for the Iranian nation to be accused of savage acts, watching."

Khomeini in another speech condemning "the great Satan" -- the United States -- played down the power of Washington to intervene militarily in Iran.

"The U.S. is too far from us to take any military action," he said. "If they had any power they would have kept the shah in power."

Khomeini's intervention today came as the Revolutionary Council instructed ministers of the outgoing Bazargan government to stay at that post for the next few days.

The council has given no hint yet of the structure of government or who is to fill the major portfolios.

Bazargan returned to the prime minister's office today for a brief farewell meeting with the staff in which he is understood to have made a number of scathing references to the clergy-controlled assembly of constitutional experts.

At a later meeting with the press, Bazargan said that he had not resigned over the occupation of the U.S. Embassy but because of the division of power between different revolutionary bodies in the Islamic republic.