RUSSIAN PRESIDENT MOVES TO CREATE A SEPARATE ARMY

President Boris N. Yeltsin ordered the creation of a separate Russian Ministry of Defense today and named himself its acting head, thus taking the first step toward the establishment of a potentially powerful Russian army.

Mr. Yeltsin's decision, which follows repeated failures within the Commonwealth of Independent States to resolve the fate of the former Soviet armed forces, appears to raise serious questions about the possibility of keeping a unified military command when the commonwealth heads of state meet in Kiev, the Ukrainian capital, on Friday.

At a news conference today, Sergei Shakhrai, Russia's Deputy Prime Minister, said the new Russian Defense Ministry would set up armed forces on Russian territory "with the view that these forces are part of the joint commonwealth armed forces and are subject to its operational command." The Message Is Clear

Yet the clear message in Mr. Yeltsin's decree, issued on his return to Moscow after a two-week vacation, is that Russia, along with several other former Soviet republics, is now ready to press its claim to the remnants of the former Soviet armed forces and to answer for its own security.

After the formal breakup of the Soviet Union last December, the leaders of the republics who formed the Commonwealth of Independent States agreed that the 3.7 million-strong former Soviet armed forces would remain unified under the command of Marshal Yevgeny I. Shaposhnikov. This was viewed as particularly important for control of the nuclear weapons spread around the former Soviet Union.

But Marshal Shaposhnikov's authority has been repeatedly challenged by Ukraine, which has set out to form its own large force, and Azerbaijan, Belarus and Moldova, all of which have taken steps to form their own military forces. Russia Moves in Germany

Ukraine's insistence on putting the important Black Sea fleet under its jurisdiction has riled Mr. Yeltsin, and it is thought that by forming his own Russian armed forces he will be in a better position to bargain with Leonid Kravchuk, the Ukrainian leader, at the commonwealth meeting on Friday.

It is always possible that a agreement can be reached by the commonwealth leaders for some form of joint military command, in which the various republican contingents under their own flags could work together, but in the current atmosphere, marked by Ukrainian independent fervor, this is seen as increasingly hard to achieve.

Russia has already moved to assume jurisdiction over former Soviet troops still in Germany and others in Poland, Mongolia and Cuba, a spokesman at the headquarters of the western group of troops told the Itar-Tass agency. "However, before the Russian Defense Ministry is formed, they will continue to be subordinate to the Commander in Chief of the Commonwealth armed forces," the spokesman was quoted as saying.

Russia is also sending a delegation to other commonwealth states to negotiate the status of troops on their territory, the television news reported this evening.

In the Russian Parliament today, Gen. Dmitri Volkogonov, a military aide to President Yeltsin, said Russia could have 1.5 million men under its command within two years.

Russia is now following a trend that became apparent shortly after the commonwealth was formed late last year, when Ukraine, Moldova and Azerbaijan declared their intention to maintain independent armies. Belarus is also considering setting up its own armed forces, and today the President of Kazakhstan, Nursultan A. Nazarbayev, issued a decree setting up republican guard units, a special military force subordinate to the President.

Until now, Russia has pressed for a unified command over conventional forces. While these are largely dependent on Russia for financial support, the idea created the impression of a common defense and ducked the tricky question of how to divide up the powerful Soviet military machine.

But Ukraine has argued that Russia is simply using the commonwealth as a cover for its own ambitions. Indeed, Ukraine's proposal to take over the nonstrategic part of the Black Sea Fleet, based in the Crimean port of Sevastopol, turned into a bitter dispute with Russia, where many people still regard Crimea and the fleet as Russian property.

Ukraine again displayed its distrust of Russia's handling of military matters last week when President Kravchuk suspended the transfer of tactical nuclear weapons to Russia, where they are to be destroyed in accordance with treaties with the United States. Mr. Kravchuk said he was given no guarantee that the weapons were in fact being destroyed, and pointed to the danger that they might "fall into the wrong hands."

Military issues are once again the main matters to be discussed when the heads of the commonwealth states gather in Kiev. According to Russian press reports, an agreement is unlikely.

"Again, as at previous summits, there is not enough time for anything serious," said a commentator in the newspaper Nezavisimaya Gazeta. Most experts agree that the mutual suspicions, particularly between Russia and Ukraine, have already overwhelmed the military debate, leaving "presidents to issue decrees, commanders to issue orders and the resulting contradictions to be decided according to the evolving C.I.S. tradition: by use of force," the commentator concluded.

As the heads of state gather to discuss the fate of the military, its future has already been decided in many parts of the former Soviet Union by individual commanders, who have begun to turn over their forces to local political leaders and in some cases are reported to have put their weapons up for sale.

An armed forces spokesman in Moscow today denied reports that two nuclear warheads had been sold to Iran from a base in Kazakhstan. Kazakhstan is one of four former Soviet republics holding nuclear weapons.