Austria's APA news agency said Waldheim, who also served as Austrian president, died of heart failure on Thursday.
Waldheim was UN chief from 1972 until 1982 and then president of Austria from 1986 to 1992.
[Waldheim, right, preached his Christian vision of the world as the UN chief [EPA]
During that time he was criticised over his wartime links to Nazi Germany's officer corps.
He admitted concealing his service with the German army in the Balkans but always denied knowing of Nazi war crimes committed there at the time, including deportations of thousands of Greek Jews.
As UN secretary-general, Waldheim preached his "Christian vision of the world".
He helped organise international conferences and pop concerts for the people of Cambodia.
But controversy erupted in March 1986 during the presidential elections campaign when an Austrian magazine published a photocopy of his 1939 German army service record.
It revealed he had been a member of the SA, the Nazi party's political militia, since 1938, the year Austria was annexed by Germany.
Most Austrians did not believe Waldheim was linked to Nazi atrocities. In fact, the accusations boosted his poll ratings as president.
But they also made him unpopular in many countries and he made almost no state visits during his tenure as Austrian president.
His victory prompted Israel to recall its ambassador and boycott his inauguration.
The US put Waldheim on its "watch list" of potential undesirables in April 1987 while scores of other countries boycotted him.
Increasingly isolated internationally and at home, he fell back on responses also given by many former Nazis: "I was only doing my duty" and "I have only obeyed orders".
Waldheim said later the furore around his presidency had a worthwhile impact in forcing Austrians to face up to the fact that they were not all passive victims of Nazi Germany.
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