"We are a nation with a big heart," said Sutiyoso. "We have to forgive, even more so because the problem was only a technical problem."
Indonesia demanded an explanation from Australia after Sydney police tried to deliver a summons to Sutiyoso in his hotel room requesting that he give evidence at an inquest into the death of an Australia-based journalist in East Timor in 1975.
The governor of Indonesia's capital city said on Wednesday that police used a master key to enter his hotel room.
The row prompted a demonstration outside the Australian embassy in Jarkata, with Indonesian protesters demanding an apology.
Sutiyoso, who was scheduled to visit Canberra after Sydney, cut short his visit and flew back to Jakarta early on Wednesday, saying he felt "slighted by such treatment".
A spokesman for Susilo Bambang Yudhoyono, the Indonesian president, said the president was "surprised" at the incident and expected that Australia would clarify the matter.
John Howard, Australia's prime minister, also sought to calm the row saying that, while coroners conducting inquests acted independently of the government, "proper courtesy should be extended" when they carried out their work.
Sutiyoso served in the Indonesian military for three decades and was part of Indonesia's occupation of the half-island nation.
The inquest in Sydney is probing the death of a cameraman who was among five British, Australian and New Zealand newsmen killed in the border town of Balibo, in East Timor, ahead of the Indonesian military's invasion in 1975.