More than 50 detainees walked out of the Becora jail on Wednesday, including rebel leader Major Alfredo Reinado, renewing concerns about security in the fledgling nation.
The escape prompted Jose Ramos-Horta on Friday to question why Australian peacekeepers had not provided more security.
"I am personally just puzzled why in spite of our repeated requests for static forces to be outside the prison, this was not done," Ramos-Horta told Australian Broadcasting Corporation radio.
"Had there been strong security outside, this could have been prevented," he said.
But John Howard, the Australian prime minister, rejected the suggestion and said the Australian peacekeepers, led by Brigadier Michael Slater, had done nothing wrong, adding it was not their job to provide jail security.
"I understand that the attitude taken by Brigadier Slater has been that it's not the role of the military to provide static guards, it's the role of the military to provide patrols," Howard said.
Reinado was one of the figureheads of a revolt that plunged the former Portuguese colony into chaos in May, prompting Australia to lead an international peacekeeping force to restore order in East Timor.
International troops and police continued their, so far fruitless, search for the escapees on Friday after Reinado said in a video recording that he did not want to stage a new revolt.
The prisoners walked out of the jail's front gate during visiting hours, security officials said.
The diplomatic spat between the two prime ministers came amid fresh clashes in Dili between armed gangs fighting with stones and arrows.
At least six people were wounded in the clashes outside a downtown Dili hotel on Friday before international security forces arrived to restore order.