Australia has made a last-minute plea for a stay in the imminent execution of two Australian drug traffickers in Indonesia, saying reports their trial had been tainted by corruption needed to be investigated.

The call from Foreign Minister Julie Bishop almost immediately deepened a diplomatic row with Jakarta.

Ms Bishop said the allegations that judges requested money to commute the death sentences for the pair were "very serious" and called into question the integrity of the sentencing process.

Indonesian President Joko Widodo said such concerns should have been conveyed years ago when the case went through the courts.

"Why didn't they raise it before, when it happens for example?" he said.

Indonesia's foreign ministry said Australians Myuran Sukumaran and Andrew Chan had been given all the legal avenues to challenge their death sentences.

The two are among nine drug convicts, including others from Brazil, Philippines, Nigeria and Indonesia, who are due to be executed by firing squad in a matter of days.