KOCEVSKI ROG, Yugoslavia, July 8— After the discovery of masses of human bones in secret graves in caves here and nearby over the last two weeks, a series of witnesses have come forward to report seeing large-scale shootings 45 years ago, painting a grisly picture of mass murder by the Communist Partisans led by Marshal Tito.
The revelations are certain to produce an emotional re-evaluation of the Partisans, of Marshal Tito and of the Communist Government he dominated for 35 years until his death in 1980.
The evidence of the killings of thousands of Yugoslavs by other Yugoslavs, emerging within weeks of the inauguration of non-Commmunist Governments in the Yugoslav republics of Slovenia and Croatia, will reopen old wounds.
Ethnic Tensions Worsening
Ethnic tensions have been growing in this country of many nationalities, which were long held together by Marshal Tito's strong leadership, Communist Party propaganda and a police presence. Some Yugoslavs fear the effect of the atrocities now being brought into the open.
After Yugoslavia was invaded in April 1941 by the Germans, Italians, Hungarians and Bulgarians, the country was torn by guerrilla warfare. An estmated total of 1,700,000 Yugoslavs were killed, both in combat and in atrocities and reprisals by and against civilians.
The fighting pitted Germans, Italians and other occupation forces, allied with a Croatian fascist movement called the Ustashi, which governed a puppet state, against the Partisans and the Serbian royalist Chetnik movement.
The Partisans and Chetniks fought against each other as well as against the Ustashi and the foreign invaders. #45 Years of Frightened Silence The evidence of the Partisan atrocities lies in masses of human bones found at the bottom of caves in Slovenia and Croatia and statements by witnesses who, after 45 years of frightened silence, have come forward.
''I drove a busload of wounded Croatian soldiers from Holy Spirit Hospital in Zagreb to Sosice in the last half of May 1945, after the war ended,'' said Branko Mulic, a 79-year-old ex-Partisan.
He disclosed the site of a mass grave in a cave near Sosice, a Croatian village. ''I watched Partisan officers line them up and, one by one, bring them to the hole in the roof of the cave, shoot them in the back of the head and let their bodies fall into the pile at the bottom. The officers alternated who did the shooting so their guns would not overheat,'' Mr. Mulic said.
Bones and Rope Bindings
Skulls with holes at the back, bullet fragments, crutches and wrist and arm bones bound with rope are all clearly visible in the remains, said Nikola Solic, one of a team of journalists from the Zagreb newspaper Vjesnik.
They used spelunkers' gear to descend the cave's sheer limestone walls to reach the bones, about 120 feet below the surface. The depth of the pile of bones is still unknown, he said.
''As far as I know, they came every day for two weeks and from time to time thereafter,'' said Jela Smeciklas, 80, a woman who said that she saw people being transported to the cave in trucks while she was tilling a plot. ''I heard more screaming than shooting, and there was a lot of shooting.''
''I could hear the voices of men, women and children,'' she said. ''Night and day they came. We heard the screams at night.''
Several Killing Sites Known
The Sosice cave is just one of several known sites where Communist Partisans settled accounts with members of the Ustasi, who themselves were responsible for mass killings of Serbs, Jews and gypsies during the war.
But historians and witnesses say most of the Partisans' victims in 1945 were Croats, Slovenes and Serbs drafted into armies allied with the Axis occupation forces amd members of the Cetnik movement. In addition to combat personnel, nurses, nuns and children were killed.
Since the news of the Sosice cave broke in Croatia last week, people from throughout Yugoslavia have been telephoning Vjesnik to report mass graves and massacre sites, said Silvije Tomasevic, a Vjesnik editor.
Historians have estimated that the Partisans shot from 70,000 to 100,000 people without trial within weeks of the war's end.
Reports by anti-Communist emigres that about 500,000 people were killed are exaggerations, said Darko Bekic, a historian in Zagreb whose father narrowly escaped one of the massacres.
Victims Turned Back by British
Most of the victims were people who fled or were trying to flee at the end of the war, Mr. Bekic said. They were returned by British troops from detention camps in Austria or were turned back at the border by British troops occupying southern Austria and northeastern Italy, Mr. Bekic said.
On the basis of the limited evidence now available, the Sosice cave contains 4,000 to 5,000 victims, most of whom were wounded soldiers brought from hospitals in and around Zagreb, Mr. Bekic added.
He discounted some reports that the cave might contain the remains of as many as 40,000 people. ''Nobody knows for sure,'' he said. ''The Government must excavate it to find out the real answer.''
Croatia's new Parliament announced this week that it would form a committee, including foreign experts, to investigate the cave and Croatia's overall casualties.
While accounts of postwar Partisan atrocities have been published in the West since the war and in Slovenia for the last six months, the issue was made public in Croatia only after the disclosure of the Sosice grave last week.
''There has been a change in the chief of police and people no longer fear repercussions,'' said Milovan Sibl, a Croatian spokesman. ''It wasn't in the interests of the old regime to expose the caves, not because of Communism, but because the victims were Croats and the Government would then no longer be able to pin the blame for the Ustasi crimes on the Croatian people as a whole.''
During the war, nationalist and religious enmity erupted throughout the country, driving members of virtually all the country's nationalities to commit acts of brutality.
Yugoslavs Killed by Yugoslavs
Most of the nation's war dead were killed by other Yugoslavs. The Ustashi championed Croatian separatism. while the Chetniks were largely in Serbia, which had dominated the new Yugoslav state during the period between the world wars. Only the Partisans tended to cut across the country's ethnic divisions.
In the postwar era, Marshal Tito, himself half-Croatian, reorganized the country on a federal basis, in which each republic nominally exercised a wide degree of autonomy. Nevertheless, until his death, the one-party Communist Government kept most real authority in its hands.
To underpin its legitimacy, it fostered an image of Marshal Tito and the Partisans as humane, heroic liberators of all of Yugoslavia's people from fascism and nationalism.
''When I heard that Partisans carried out the killings, it made my head spin because it went against everything I heard in school,'' said Nikola Hranilovic, a Sosice resident who said he learned of the killings years ago but kept silent because he feared the police.
''I always heard that the Partisans fought for our side and for our people. It never became clear to me why they did this to women and men who were forced to join the army.''
Both Croatian and Slovene officials and journalists have expressed concern that the disclosure of the mass graves might worsen the already-tense national relations within Yugoslavia, especially between Croats and Serbs.
Requiem Mass Near Caves
Today in a clearing in Kocevski Rog, in a mountain region about 45 miles south of Ljubljana, Archbishop Alojzij Sustar, President Milan Kucan of Slovenia and 30,000 Slovenes took part in a requiem Mass and reconciliation ceremony. Two nearby caves contain the remains of as many as 16,000 Slovenes and Croats. Croats conducted similar rites in Sosice.
Some Partisan veterans have already condemned these commemorations as anti-patriotic. The press in Serbia and other Communist-ruled republics has scarcely mentioned the issue.
''It would be the worst situation to turn this into another cycle of vengeance,'' said Hido Biscevic, Vjesnik's chief editor. ''Until now, the political system was able to hide it and now it can't be hidden anymore. But we must see that it does not lead to new instability.''
''Serbs and Croats will all be better off if they adopt the old Indian practice and bury the hatchet forever,'' Mr. Mulic said. ''They should realize that we are not born as Serbs and Croats, but naked.''
Photo: A mass grave recently unearthed in Sosice, Yugoslavia. Witnesses who have come forward since the discovery say large-scale shootings by Communists led by Marshal Tito took place in the area 45 years ago. (Nikola Solic/Vjesnik); map of Yugoslavia showing location of Kocevski Rog.