Prime Minister Tony Abbott has said he was recalling nation's ambassador to Indonesia in protest against the execution of two Australian drug smugglers.

"We respect Indonesia's sovereignty, but we do deplore what's been done and this cannot be simply business as usual," Abbott told reporters in Canberra.

"I want to stress that this is a very important relationship between Australia and Indonesia but it has suffered as a result of what's been done over the last few hours."

Australians Myuran Sukumaran and Andrew Chan were executed by firing squad along with six other drug convicts from several countries shortly after midnight on Wednesday 28 April, local media said.

Ambassador Paul Gibson will return to Australia at the end of the week, Foreign Minister Julie Bishop said.