Myuran Sukumaran and Andrew Chan, the ringleaders of the so-called "Bali Nine" drug smuggling gang, were arrested for trying to traffic heroin out of Indonesia in 2005 and sentenced to death the following year.
Their appeals for presidential clemency, typically a death row convict's final chance of avoiding the firing squad, were rejected by new Indonesian President Joko Widodo in recent months.
On Tuesday, the Administrative Court in Jakarta dismissed the men's application to challenge Widodo's refusal to grant them clemency, a rare move that was seen as having little chance of success.
He also rejected Chan's application. The judge said that the pair had 14 days to lodge an appeal, and their lawyers said they would.
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The pair's legal team had earlier applied for a second judicial review of their cases, but judges also rejected that application.
Authorities originally said the pair would be put to death in February but last week announced that their executions would be delayed by up to a month. They blamed "technical reasons", insisting that sustained diplomatic pressure from Canberra had nothing to do with the decision.
Their legal team have argued that they have been rehabilitated in prison and Widodo had failed to consider the cases properly.
It is not clear when the pair will be put to death, although the head of the prosecutor's office on Bali, where the pair are in prison, previously said it is "very likely" that they will be transferred this week to an island off Java where the executions will take place.
The looming executions have dramatically heightened tensions between Australia and Indonesia, fraying ties that were only just recovering from a spying row.
Chan and Sukumaran are among seven foreigners -- including citizens from France, Ghana, Brazil and Nigeria -- who have lost their appeals for presidential clemency, the final hope of avoiding the firing squad.