The country will send a team of ministers to attend the funeral of the Catholic leader.
"On behalf of the Government and the Indonesian people, I convey a deep condolence with the death of Pope John Paul II," President Susilo Bambang Yudhoyono said in a press conference before leaving Jakarta to Australia for a two-day state visit, which will proceed to New Zealand and East Timor.
Yudhoyono said the government will send a team of high-ranking officials, led by Welfare Minister Alwi Shihab to attend the Pope's funeral.
Nearly 90 per cent of the country's 215 million people are Muslims, making Indonesia the world's largest Islamic nation. But the state ideology preaches religious tolerance and recognizes other religions as well.