Myuran Sukumaran and Andrew Chan committed their crime at the same time, which is why they will face simultaneous execution, Prasetyo said, according to the news agency AFP.
"When a crime is committed by more than one person, the execution must be conducted at the same time. So Myuran will wait for his turn," Prasetyo said.
"This will send a message to members of drugs syndicates — there is no mercy for drug dealers and traffickers. For those who disagree with the death penalty, hopefully they can understand that what we are doing is simply to save our nation from the threat of narcotics," he added.
Sukumaran was one of nine Australian citizens who were detained in Bali in April 2005 with more than 8.3 kg (18lb) of heroin. This group became known as the "Bali Nine".
Sukumaran and Chan were named as the ringleaders of the group and were sentenced to death in 2006. One of the remaining seven is serving a 20-year sentence and the others are serving life in prison.
Although the date for the execution of Sukumaran and Chan is yet to be set, six other people, including five foreigners from Brazil, Malawi, Vietnam and Nigeria, will be put to death in Indonesia this Sunday for their involvement in drug trafficking-related cases.
Chan is currently waiting for Indonesian President Joko Widodo to respond to his appeal for a pardon.
The executions will mark the first use of capital punishment since President Widodo took office in October 2014.
After Indonesia resumed executions in 2013 following a four-year moratorium, President Widodo pledged not to grant clemency to anyone who was convicted to death due to drug-related crimes.
Meanwhile, rights group Amnesty International has called on Indonesia to put a halt to the executions and abandon capital punishment altogether.
