"We would like to express our sympathy over the past violence that have claimed lives and material losses," Yudhoyono said in Bali after receiving the final report from the two nations' Commission for Truth and Friendship, Antara news agency reported. Timor-Leste President Ramos Horta also received the report.
The 1999 referendum was for Timor-Leste's independence from Indonesia, which had occupied it for more than two decades. But the period leading up to the referendum resulted in hundreds being killed, raped and tortured.
"I believe that from this report the relations between the two countries will remain strong," Yudhoyono said.
Ramos Horta was quoted as saying the report could improve the spirit of mutual forgiveness and improve relations between the two countries.
The BBC said the report details the violations with the Indonesian army taking much of the blame. The United Nations, which blamed Indonesia for the violations, has demanded those guilty be brought to justice.