The U.N. War Crimes Commission concluded in 1948 that there was sufficient evidence to prosecute Kurt Waldheim for the murder of Yugoslav partisans during World War II, and it put him on its top priority "A" list of persons who should be brought to trial, according to a secret U.N. file obtained by The Washington Post yesterday.

The file, based on a report prepared in late 1947 by an official Yugoslav war crimes commission, alleges that Waldheim was involved in "murder" and "putting hostages to death" from April 1944 to May 1945. The U.N. commission said that after examining the facts, it believed that "a clear prima facie case had been presented" and that Waldheim "should be delivered up for trial."

The allegations in the U.N. file have been a key element in the controversy over Waldheim's wartime activities as a German army officer in the Balkans. Details of the charges were made public by a Yugoslav newspaper last month, but the United Nations has kept the file secret, while giving copies to the Israeli and Austrian governments on April 9 under a pledge of confidentiality.

Waldheim, who was U.N. secretary general from 1972 to 1982, has called the charges in the U.N. dossier false and has denied any involvement in war crimes during his military service in Yugoslavia and Greece from 1942 to 1945.

Why the U.N. file obtained by The Post yesterday remained undiscovered in the U.N.'s archives in New York for almost four decades is a mystery. It came to light last month after the World Jewish Congress discovered other documents raising questions about Waldheim's wartime role.

Waldheim is a candidate for president of Austria in elections to be held May 4. The current president, Rudolph Kirchschlaeger, went on Austrian television yesterday to say that after examining the U.N. file and other documents provided by the World Jewish Congress, he could not make a judgment about Waldheim's guilt or innocence.

However, Kirchschlaeger, a widely respected former jurist, said that if he were in the position of a prosecutor, "on the basis of the evidence presented to me . . . I would not dare to file an indictment in a regular court."

Kirchschlaeger said he would simply present the Austrian people a summary of the facts. He added: "Whatever conclusions you draw for the presidential election . . . must be left to you alone."

The U.N. file is one of 40,000 sealed dossiers on war crimes suspects compiled by the 17-nation commission that operated in London from 1943 to 1948. In Waldheim's case, the commission followed its standard practice of summarizing the charges presented against him, weighing the evidence against international legal norms, and rendering a judgment about whether the case merited prosecution.

The original Yugoslav report was returned to the Belgrade government, and is not part of the U.N. file. The Yugoslav government took no further action against Waldheim. No explanation for its decision to drop the matter has ever been offered.

According to the U.N. documents, Yugoslavia charged that Waldheim was a first lieutenant on the intelligence staff of the German Army Group E and was involved in directing retaliations that "were the means for the massacre of numerous sections of the Serb population."

In support of the charges, it quoted a clerk in Waldheim's division, Johann Mayer, as telling Yugoslav authorities that Waldheim was the deputy to his section commander. Mayer's testimony added:

"[Waldheim's] duties were those of an intelligence officer. It was up to him to bring up suggestions concerning reprisal actions, treatment of prisoners of war and civilian internees . . . . I remember certain persons having been murdered at Sarajevo in November 1944. They were executed according to the order given by Waldheim in retaliation for desertion from the German army of some other persons . . . . "

The documents said another witness, Klaus Melinschoff, who is not otherwise identified, "stated that measures of reprisal and retaliation were applied by the German general staff and high-ranking German officers. The same line of action was taken by the accused Waldheim ."

Waldheim and his son, Gerhard, who is in the United States to plead his father's case, have said several times that the charges are false and unjustified because the principal witness, Mayer, was an unreliable individual who was convicted five times of crimes in Austria.

In an interview in the current issue of U.S. News & World Report, Waldheim said Mayer "was not even working in my department. He tried to save his skin apparently, by making such statements, which are completely unfounded . . . . He unfortunately is dead. I have a number of witnesses who knew the man. He was highly unreliable. There are many inaccuracies in that file."

Waldheim has noted that after the war, he visited Yugoslavia several times as an Austrian diplomat and as U.N. secretary general and was received by Yugoslavia's late president, Marshal Tito.

He also pointed out that Yugoslavia never pursued the charges against him and that the present Yugoslav government has maintained silence throughout the controversy over his war record.

However, in 1948 the U.N. commission decided that Waldheim should be given its highest classification, "A," which was reserved for suspects against whom the commission believed there was a clear-cut case meriting prosecution. Waldheim's 14-page file was listed as "79/724," meaning he was the 724th person put on the 79th list of war-crimes suspects compiled by the commission.

Some U.N. officials have speculated privately that the file "fell between the cracks" and gathered dust in the archives for so long because Waldheim, in his memoirs and other biographical statements, concealed the fact that he had served in the Balkans, instead saying that he spent the last years of the war as a student in Vienna.

As a result, officials said, there was no reason to look for the file even when Waldheim became a candidate for secretary general in 1971.

Other observers have noted that the Yugoslav charges were made when Yugoslavia, now an independent communist state, was a satellite of the Soviet Union. They theorize that in the Cold War climate of that time, officials of the United States and other western countries concentrated on war crimes committed in western Europe and did not give much priority and attention to persons sought by the communist bloc.