Iran's armed forces chief of staff, Gen. Nasser Farbod, resigned today in disagreement with revolutionary authorities over the army's role in domestic affairs.

His resignation followed a limited merger between the beleaguered Cabinet of Prime Minister Mehdi Bazargan and the powerful Revolutionary Council under Ayatollah Ruhollah Khomeini, Aimed, according to officials, at strengthening government authority, the move could herald a tougher policy toward autonomy-seeking regional minorities, observers here said.

Gen. Farbod complained of interference from outside the government in a thinly veiled reference to the Revolutionary Council, which had just appointed a clergyman as an under-secretary of defense.

The role of the Revolutionary Guards - and elite force which answers only to Ayatollah Ruhollah Khomeini and his ruling Revolutionary Council - also has been a sore point with many senior military commanders who seek to rebuild the regular army.

The main issue in Farbod's resignation, however, was the use of troops against ethnic minorities.

"They wanted to take the army against the people and I refused," Farbod said. "I don't like at all to use the army against these people. These are political differences."

There has also been evidence of resistance among troops to carrying out internal security operations after the revolution. Similar actions earned the death penalty for some soldiers who obeyed the orders of the shah's officers and opened fire on demonstrators during the upheaval against the monarchy.

Farboh, indicated, however, that the authorities intended to use the army further in dealing with these difficulties.

Also leaving office today was Iran's controversial military police chief, Gen. Self Amir Rahimi, one of the strongest advocates of military intervention in the provinces. He was fired Thursday after his charges that military commanders were plotting against Khomeini's rule caused, an uproar.

At a press conference before leaving his Tehran barracks, Rahimi said the only reason given for his dismissal was that he talked publicly on political affairs. He said, "Anywhere in the world a general who sees the country burning and falling apart would speak if not scream."

Prime Minister Bazargan reportedly appointed Rahimi as military attache in Paris, but the general said he had refused the job and the government later denied making such an appointment.

Meanwhile, a major test of the government's approach to minorities arose with fresh fighting between Iranian Kurds and Turks in the province of West Azerbaijan.

The fighting broke out two days ago when gendarmes tried to reopen a border post near the town of Saro with the help of Turkish-speaking militiamen. Hostility between the Kurds and Turks has been running high since fighting between them in April left more than 500 dead.

Units of the army's 64th Division backed by tanks and artillery have been sent to relieve the besieged border post, according to Kurdish sources who also reported coming under attack from helicopter gunships.

Stiff resistance is being mounted by Kurdish groups equipped, according to both the army and Kurdish political organizations, with antiaircraft and antitank guns.

The Kurds claim that some soldiers have surrendered rather than fight against them. They also say they have taken several Turkish militiamen hostage.

In a separate development in Tehran, a gunman assassinated a clergyman, Seyyed Mohsen Behbahani, who was a broadcaster on religious affairs during the shah's regime.

Behbahani, the fourth assassination victim since the revolution, was shot in the head when he answered the door of his north Tehran home. The gunman escaped on a motorcycle.