Myuran Sukumaran was one of nine Australians arrested in 2005 for attempting to smuggle eight kilograms of heroin out of the Indonesian resort island of Bali.
"The presidential decree signed on December 30 stipulates that the clemency of an Australian on death row, Myuran Sukumaran, has been rejected," Hasoloan Sianturi, a spokesman for the court in Bali with jurisdiction for the case, told AFP.
Sukumaran and another member of the so-called "Bali Nine" who was sentenced to death, Andrew Chan, lodged appeals for presidential clemency after their final court appeals were rejected in 2011.
Sianturi said the court received the presidential decision yesterday, but there was no information available on Chan's appeal.
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The other seven members of the "Bali Nine" were given life sentences. One of them later had her sentenced reduced to 20 years.
Indonesia enforces some of the world's toughest punishments for narcotics offences and there is strong public support for executing drug traffickers.
New President Joko Widodo pledged in December, shortly after taking office, there would be no pardons for drug traffickers on death row, including foreigners.
Five more foreigners, from Hong Kong and Malaysia, were arrested this week as they allegedly tried to smuggle 860 kilograms of crystal methamphetamines through a port near the capital of Jakarta.