In a sudden, sharp departure from official Kremlin support of the Iranian revolution, the Soviet government newspaper Izvestia has labeled Ayatollah Ruhollah Khomeini's rule a disaster for Iran that has brought only economic chaos, political persecution and fanatical repression of national minorities.

The damning indictment of Khomeini by Alexander Bovin, widely regarded here and abroad as the Soviet Union's most sophisticated and best informed political commentator, is a clear signal of deep Kremlin anxiety about the continuing turmoil in its oilrich neighbor and anger at Khomeini's repeated calls for cleansing the country of pro-Communists.

The Bovin article in Izvestia's weekly review Nedelya (Week), comes at a time when the United States, through shipments of heating and fuel oil and the readying of new arms supplies to Tehran, appears from here to be subtly reasserting its influence in the strategic Persian Gulf state at the expense of Moscow.

Bovin made no reference to the United States in his article, concentrating instead on a broad attack on Khomeini and the Islamic fundamentalism being directed from the religious city of Qom, the Ayatollah's headquarters.

"The coalition of political movements which insured the victory of the revolution has already collapsed," Bovin wrote. "The interim government, without authority or will for power, is practically paralyzed."

Bovin questioned whether Khomeini's religious fanaticism can bring order to the country, and he further obliquely criticized the religious leader for apparently spurning Soviet offers of aid and attempts to open direct lines to the revolutionaries running the country.

The commentator asserted that "one can obviously doubt that the theocratic conception of the state will help Iran become a modern and flourishing country. It is obvious to me that fanning of religious fanatics, the anti-Communist hysteria and attempts to show in a false light the policies and intentions of a friendly country will not bring fruit to the Iranian people."

Communists have been blamed by the Khomeini government for fomenting revolt in Kurdistan in northwest Iran. The Soviets have denied aiding Kurdish rebels who seek autonomy, although Soviet designs on the area date back to the waning days of World War II. Bovin left little doubt where the Kremlin's sympathies lie, however.

"Today, the war in Kurdistan continues," wrote Bovin. "The activities of other ethnic groups are supressed. Those who demand equal rights and autonomy are being denounced as traitors. They are being executed and the religion of Shiite (a Moslem sect headed in Iran by Khomeini) is being forced on them."

About 3 1/2 million Kurds a majority of them Sunni Moslems, are concentrated in the rugged northwest portion of Iran, bordered by the Soviet Union. To the north and Turkey and Iraq to the west. Sheik Ezzedin Husseni, spiritual leader of the Sunni Kurds, has been labelled "satanic" by Khomeini and accused of seeking to form a secessionist Communist state. The sheik and other Kurdish leaders are in hiding, reportedly on the Iran-Iraq border following the fall of Mahabad to Ikranian units loyal to Khomeini.

Bovin's denuniciation headlined "With the Koran and Sabre," lays a series of specific charges at the ayatollah's feet.

"Economic chaos continues," Bovin said. "All publishing houses in which there is a difference with the reigning religious doctrine are prohibited. Under the guise of 'hunting for Communists,' people who support progressive social change are being repressed. . ."

The revolution's shortcomings are not just the product of revolutionary mistakes but go deeper, Bovin asserted. He quoted statements by Khomeini and his followers that pledge death to all who resist Islam and the triumph of Islamic liberation movements in Afgahnistan and elsewhere. The Soviets are involved deeply in trying to save the Marxist government of Afghani leader Nur Mohammed Taraki in the face of fierce guerrilla warefare by Islamic tribesmen.

Soviet commentary on the Iranian revolution, warm and laudatory after an initial period of cautious noncommitment has become more critical in recent months as the Khomeini government continued to label Communists enemies of the new Islamic state. The drift of official Soviet presentation of Iran to a less-than-perfect neighbor quickened during the summer.

For example, on June 1, the Communist Party daily Pravda and other key central newspapers in lengthy articles lauded various mutual aid projects of the two countries, bombarding readers with facts and figures about natural gas to be shipped from Iran to the Soviet Union and new steel mills to be built in Iran by the Soviets.

But by late last month, the Soviet tone had turned far more critical in the face of Khomeini's attacks on the Taraki government in Kabul and on Soviet support for it.

Pravda on Aug. 22 complained that the Khomeini-controlled Iranian press had slandered Afghanistan and the Soviet Union by accusing them of fomenting troubles for Islam. But the Pravda attack fell far short of a personal indictment against the ayatollah, which the Bovin article in the current Nedelya makes.

The Bovin article also brings the tone of Soviet displeasure to a new level. That it appeared in Nedelya is considered significant here as a sign of the authoritativeness of his stated views. The article seems to point to further troubles to come between the Kremlin and Khomeini.