On appeals, the court imposed the death penalty on Scott Rush, 20, Tan Duc Thanh Nguyen, 23, Si Yi Chen, 21, and Matthew Norman, 19.
The four originally had been sentenced to either life imprisonment or 20 years in jail for their role in a heroin smuggling ring.
The four will be hoping a judicial review, or presidential clemency, will now spare their lives.
Senior Liberal backbencher Bruce Baird, who is chairman of the Amnesty International parliamentary group, said Australia should not sit back and accept the death penalties on members of the Bali Nine.
"We will be making representations to the embassy here in Canberra," Mr Baird told reporters in Canberra today. "It is a great concern that we would have six young Australians facing the death penalty.
"I do think this far too excessive and it's time that there is a recognition by Indonesia that we are a firm friend of theirs but we don't expect our young people to receive the death penalty. It's totally unacceptable."
Justice Minister Chris Ellison said the death sentences would be strongly appealed by the federal government.
"We will certainly make strong pleas for clemency," Senator Ellison told the Nine Network. "The Australian government has for many years gone into bat where someone has faced the death penalty ... we will continue to do that."
However, Senator Ellison said there was a process to go through before a direct plea for clemency and, like Foreign Minister Alexander Downer, he ruled out the idea the death sentences could harm relations between Indonesia and Australia.
"We have a strong relationship with Indonesia ... I think our relationship can survive."
'No sympathy'
But Liberal backbencher Wilson Tuckey said he had no sympathy for the Bali Nine members, saying they risked killing Australians if they had smuggled heroin into the country.
"No, I haven't. They've had no sympathy for thousands of young people in Australia who may have even died," Mr Tuckey said.
"We had 1,000 Australians die one year not that long back from drug overdose and the statistics are alarming ... now they had no care for those people, so why should Australians have care for them?"
Mr Tuckey hoped Indonesia would apply similar penalties to some of the Bali bombers.
"I trust, nevertheless, that some Bali bombers have been dealt with in a similar fashion prior to that event (the execution of Australians)," Mr Tuckey said.
Rush, Nguyen, Chen and Norman now join Bali Nine ringleaders Andrew Chan, 22, and Myuran Sukumaran, 25, on death row for their role in attempting to smuggle 8.3kg of heroin to Australia last April.
The Supreme Court, Indonesia's highest judicial authority, also confirmed the death sentences for Chan and Sukumaran.
It imposed life sentences on drug mules Michael Czugaj, 21, and Martin Stephens, 30.
The final member of the Nine, Renae Lawrence, 28, is serving 20 years after her life term was cut earlier. She is the only one of the Bali Nine not subject to an appeal.
Norman's mother
The mother of Bali Nine drug runner Matthew Norman said she will move to Indonesia to support her son who is now facing death by firing squad.
"I'm actually going to move over to Bali around Christmas time to spend quality time with him," Norman's mother Robyn Davis told Southern Cross Radio.
Mrs Davis said Norman's father had spoken to him since the death penalty was announced, adding "he (Norman) is a bit shocked and he doesn't believe it”.
Mrs Davis says her son is dyslexic and was not smart enough to be one of the masterminds of the drug operation.
"He hasn't got the brains to be one of the bosses ... he's always been laughing and joking around but I've never seen anything like this before. I'm not protecting the boy, he paid his own flight over so I don't understand the whole situation as yet."
"Amrozi's (one of three 2002 Bali bombers currently on death row) not dead yet and he's one of the bombers ... how can they shoot Australian kids and let this guy lived after he killed thousands of people," Mrs Davis said.
Family struggling
A family priest says the parents of Scott Rush suffered through a sad and confusing day when the news of the death penalties was confirmed yesterday.
"We were given some hope throughout the day and then by the end of the day the news was confirmed, it was a very confusing and sad day for everybody yesterday," Father Tim Harris told the Nine Network.
Rush's lawyer
The Australian lawyer for Scott Rush will travel to Jakarta tomorrow to take up legal issues in the next stage of the Australian's case.
Colin McDonald, QC said there was room to move in Rush's defence despite the Indonesian Supreme Court's decision that the 20-year-old must now face the death penalty.
"Objectively, the circumstances are obviously dire but I'm not engaged to provide negative sentiment but to move this case forward," Mr McDonald told AAP. "That's exactly what I intend to do and there is room to move here, there really is."