Paul Grigson (AFP /Gianluigi Guercia)

Prime Minister Tony Abbott on Wednesday defended his decision to send Australia's ambassador back to Jakarta, following a six-week absence in protest at the execution of two drug smugglers.

Indonesia executed Australians Andrew Chan and Myuran Sukumaran by firing squad in April, ignoring impassioned pleas from the Australian government and public.

"I made it clear that the ambassador would be withdrawn for a time because of the depth of Australia's feeling in response to those executions," Abbott said.

"We took what was a pretty unprecedented step, but he's been out of there for about 40 days and I think now is an appropriate time for him to go back."

Ambassador Paul Grigson resumed his post on Monday.

"Our relations with Indonesia are strong and getting stronger," Abbott continued.

"Obviously there was some stress as a result of the execution of two of our citizens and obviously we made the strongest possible representations at the time.

"We thought that those executions were unnecessary and counterproductive.

"But we also made it crystal clear at the time that we weren't going to let this permanently damage what is a very good friendship and a very important relationship."

Indonesia executed five other foreign drug convicts along with the Australians, igniting global condemnation.

President Joko Widodo has strongly advocated capital punishment, insisting that Indonesia faces an emergency over rising narcotics use.

Ties between the two neighbors had been slowly recovering before the executions, after sinking to their lowest point in years in late 2013 on reports that Australian spies tried to tap the phones of the president and his inner circle.

Jakarta recalled its ambassador from Canberra and suspended cooperation in several areas, including efforts to stop people-smuggling boats reaching Australia.

Australia's military-led efforts to turn back asylum-seeker boats also angered Indonesia, with tensions rising last year after the navy admitted entering the Southeast Asian nation's territorial waters.(++++)

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