The World Jewish Congress charged today that 48 hours before German army units burned three Yugoslav villages in 1944, Kurt Waldheim signed two secret intelligence reports pinpointing the area as a center of partisan activity.

The documents, while inconclusive about Waldheim's role in the burnings that killed 114 civilians, appear to support Yugoslav charges that the former U.N. secretary general was involved in antipartisan reprisals while a German army officer in the Balkans from 1942 to 1945.

Copies of the documents were found in the National Archives in Washington, the WJC said. Dated Oct. 12, 1944, they report "strengthened bandit activity on the Stip-Kocane road" and "additional bandit forces approaching the Stip-Kocane road."

Waldheim was a staff intelligence officer of the German Army Group E at the time. A 1947 report by a Yugoslav war crimes commission charged that during his group's retreat to northern Yugoslavia in October 1944, he was involved in burning the villages -- Krupiste, Gorni Balvan and Dolyni Balvan -- between Stip and Kocane.

The charges were part of the basis for a recently revealed 1948 finding by the U.N. War Crimes Commission that Waldheim should be tried as a war criminal. However, in the secret U.N. file on Waldheim, a page for detailing the Stip-Kocane incidents was inexplicably left blank.

Waldheim, who was U.N. secretary general from 1972 to 1982, is the front-running candidate in next month's runoff election for president of Austria. His war record has been an issue in the election campaign, and although he admitted concealing his war record for four decades, he has denied any involvement in war crimes. In a memo given to The Washington Post by his son, Gerhard, last month, Waldheim said the Stip-Kocane massacres took place on Oct. 20, 1944, and he denied being in the vicinity at the time.

Instead, he said, he was among several Group E staff officers evacuated by airplane to the vicinity of Mitrovica, about 200 miles north of those villages, on Oct. 13.

However, a Newsweek correspondent visited the Stip-Kocane area last month and quoted survivors as saying that the massacres occurred on Oct. 14. Twice in the preceding 48 hours Waldheim had signed intelligence reports "targeting this area as an area of bandit activity," Eli M. Rosenbaum, the WJC general counsel, said yesterday.

Rosenbaum also said that the German forces used the term "bandit" to describe partisan guerrilla groups and that Group E's standing orders called for retaliating against partisans by shooting hostages and burning property.

Although the Yugoslav government has kept its 1947 report secret, a Belgrade newspaper revealed its contents on March 26. It quoted witnesses as saying that reprisal recommendations were "made by Lieutenant Waldheim and were for the approval of his superior officer, Lt. Col. Warnstorff."

One of the documents made public by the WJC yesterday bears the notation that it was issued on Warnstorff's behalf. Waldheim's signature appears beneath that notation. Waldheim has acknowledged that he signed intelligence documents, but he also has insisted that his job was to forward papers to superior officers and that he merely certified them as "correct copies" without examining the contents.

The Belgrade newspaper also quoted the Yugoslav commission as having received "the testimony of the war criminal Egbert Hilcer that Kurt Waldheim's responsibility was reprisal committed on the way between Kocane and Stip." Waldheim contends that he never knew an Egbert Hilcer and that German army records list no such person.

Rosenbaum said "Egbert Hilcer" apparently was a misspelling of Capt. Karl-Heinz Egberts-Hilker, an infantry company commander who was executed by Yugoslavia in 1948 for taking part in the Kocane-Stip massacres.