LONDON (AP) _ A newspaper reported Sunday that Austrian President Kurt Waldheim told his publisher he served in the German army in Greece from April 1943-45. During that period some 40,000 Jews in the Balkans were deported to Nazi concentration camps.

The Sunday Express said that report contradicts previous statements by Waldheim that he was not in Greece at the time of the deportations.

It reported that in a cable to his New York publisher, Adler and Adler, Waldheim said:

''From April 1943, until Spring 1945, I served as one of the ordnance officers of the Heeresgruppe E in Arsakali, Greece.''

The newspaper said Arsakali served as the headquarters of the Nazi command at Salonika, where the deportation of Greek Jews to the Auschwitz death camp was planned and carried out during World War II.

It did not give the date of the cable message but said it was sent when there were no public allegations that Waldheim was in Greece as a German army officer. The Express also did not say how it obtained a copy of the alleged message to Adler and Adler.

Waldheim has been barred from entering the United States because of allegations about his wartime past.

Waldheim originally denied he was in the German army after 1941, but as allegations and reports mounted he said he remained in the army as a rear- echelon supply officer and low-level translator.

The Express said Adler and Adler agreed to publish Waldheim's memoirs of his years as United Nations secretary-general from 1972 to 1982 before the accusations against Waldheim emerged.

It said a draft of the memoirs claimed Waldheim was a student in Vienna from 1943 to 1945. Then, as the allegations increased, the publisher insisted Waldheim revise his account about where he was during those years, the newspaper said.

The Chicago Sun-Times reported last month that it gained access to a secret United Nations file on Waldheim that identified him as a German army intelligence officer in and around Salonika during World War II.

It said the file showed the army unit under which Waldheim served as a lieutenant was responsible for atrocities against Yugoslav partisans, the deportations of the Greek Jews and the abuse of American and other Allied prisoners in 1943.

Waldheim's name is included in a ''Wanted '' list compiled by the U.S. Army in 1947 that contains thousands of names. Next to Waldheim's name - under the column ''reason wanted,'' it says ''Murder.'' Next to the name is the number of the secret U.N. file compiled by the 17-nation U.S. War Crimes Commission after the end of the war.

The American CIA, which denied in 1980 that it had a report on Waldheim, acknowledged last month that its intelligence agents filed a report in 1945. The World Jewish Congress has failed to obtain a copy under the U.S. Freedom of Information Act.