"Kurt Waldheim will be remembered as a long-standing Secretary-General of the United Nations and an untiring champion of peace in the world," Mesic said, among other things, in his message.
Waldheim died in Vienna on Thursday from heart failure. He was 88.
Waldheim headed the world organisation from 1972 to 1982, and his election as President of Austria in 1986 was marred by a scandal following a discovery that during the Second World War he had served in a Nazi unit that committed atrocities in the Balkans.