Andrew Chan, 31, and Myuran Sukumaran, 34, were killed by firing squad on Wednesday over their role in a plot to bring heroin to Australia from the Indonesian resort island of Bali, despite international pleas to Jakarta for clemency.
Abbott said he understood the dismay and anger over the executions but respected Indonesia's sovereignty.
"It really was terrible that these cruel and unnecessary executions went ahead," he told reporters in Sydney.
"The important thing now is not to do any thing that would make a difficult situation worse."
The Department of Foreign Affairs and Trade was unable to confirm reports that the men's bodies were on a flight which touched down early Saturday in Sydney.
