"Jews were persecuted and killed in my country too only because they were Jews," Mesic said in an address at the "Remembering the Past, Shaping the Future" special assembly at Yad Vashem.
Mesic said present-day Croatia was founded on anti-fascism and guaranteed equality for every citizen.
He was one of about 30 statesmen attending the assembly.
Mesic thanked Israel for the invitation to attend the inauguration of a new Holocaust museum, saying he considered it an acknowledgement of himself as well as Croatia.
He said he would continue to fight for telling the truth about the past and condemn any attempt to cover up or forge history, no matter what it had been like.
The assembly was also addressed by the presidents of Israel, Poland, Slovakia, Switzerland, Albania, Serbia and Montenegro, and Bosnia-Herzegovina, the prime ministers of France, Sweden, Denmark, Belgium and the Netherlands, and senior officials from a dozen other countries.