Moscow — The Soviet Union, after hours of official silence, moved Thursday to counter a formal charge from the United States that it shot down a crowded civilian airliner.
But diplomats here felt the statement, if not too little, was almost surely too late to avoid a strain in Kremlin relations with the outside world.
The Soviets' long fixation with security and secrecy was seen as a major factor in the long absence of Soviet comment on the air disaster. The strict hierarchical setup of the Soviet military, meanwhile, left diplomats with little doubt any rocket attack by a Soviet pilot must almost surely have been OKed by higher authorities. This was seen as doubly likely if, as the Americans said, Soviet radar had tracked the civilian airliner for fully 21/2 hours.
Moscow's brief reply, from the official Tass news agency, said a Korean Air Lines jet had twice violated Soviet airspace. The jet ''did not have navigation lights,'' Moscow said, ''did not respond to queries . . . and did not react to signals and warnings'' from Soviet fighter jets sent up ''to give assistance in directing it to the nearest airfield.''
''It continued its flight in the direction of the Sea of Japan,'' the statement concluded.
The Tass item followed a US charge that a Soviet air force jet had downed the Boeing 747 in Soviet airspace near the fortified Asian island of Sakhalin, north of Japan.
Diplomats were virtually united on one point: that with the detailed US charge, the Kremlin risks finding its escalating ''peace campaign'' in the West seriously complicated.
Assuming the US statement was well founded, diplomats said the tragedy - and the Soviets' lengthy silence on the incident - seemed to owe much to the Soviets' long preoccupation with matters of security and secrecy.
Western data suggest the Soviet Far East - notably the Boeing's reported path from the Kamchatka Peninsula in the northeast, over the Sea of Okhotsk and Sakhalin - is a prime security area that is well fortified.
In April 1978 another South Korean airliner was fired at and forced down by fighter planes over northeast Russia. Two passengers lost their lives.
The latest incident seems so far, from all standpoints, geometrically more serious. It seemed to diplomats here by late Sept. 1 that all 269 passengers had likely perished. Beyond this, the Soviets were much more prompt in offering an official account of the 1978 incident.
Diplomats felt the political repercussions of the current tragedy could yet depend considerably on the Soviet response to the US charge. But they did suggest Soviet relations on various foreign fronts could potentially be affected. Principally, the analysts noted:
* Ties with nearby Japan have already been subject to increased strain over what the Japanese see as a worrisome Soviet military buildup in the east, and a territorial dispute over the Kurile Islands, near Sakhalin. Japan's recently elected Nakasone government has been drawing steadily closer to the Reagan administration on defense issues.
* West Europe has been the principal target of an escalating public bid by the Kremlin to portray Mr. Reagan as culprit in the arms race, and to press Soviet ''peace initiatives'' as an alternative to planned deployment of new US missiles in NATO countries beginning this December.
* And relations between Moscow and Washington, strained by wide differences on arms policy and other key issues, had recently begun to show signs of at least atmospheric improvement in other areas.
The Soviets and Americans, for instance, signed a new grain trade accord last month. Both sides had joined in a compromise at the Madrid follow-up talks on the Helsinki Final Act. And the Reagan administration, in effect cancelling an Afghan-related sanction, agreed to reopen talks on an additional superpower consular mission in each country.