Suffering from a number of serious health issues, including a heart condition and diabetes, the 66-year-old was recently transferred to the Royal Adelaide Hospital where he died late on Monday night.
The Department of Correctional Services confirmed his death but did not elaborate on the exact cause.
Perre was found guilty in June last year of the murder of Detective Sergeant Geoffrey Bowen and the attempted murder of lawyer Peter Wallis after a parcel bomb he built and sent exploded.
He recently argued an appeal before a three-judge panel submitting that his convictions couldn't be supported on the evidence and that someone else, possibly a now-dead mafia identity, could have been responsible for the attack.
Court of Appeal President Justice Mark Livesey said once Perre's death was proved, usually by a death certificate, his right of appeal would abate.
"That is sometimes described as the right of appeal dying with the appellant," Justice Livesey said.
Perre's death will now be regarded as a death in custody and will therefore be subject to a coronial inquest.
His jailing over the NCA bombing came while he was already serving time for drug offences.
In sentencing in October last year, Justice Kevin Nicholson extended Perre's non-parole period by 30 years, meaning he would have been in his mid-90s before being eligible for release.
Justice Nicholson described the murder of Det Sgt Bowen and the grievous harm caused to Mr Wallis as "violent, barbaric and ruthless".
"Your conduct was brutish. That is totally devoid of any human sensibility," he told Perre in October last year.
"It was not just premeditated but intricately devised and planned over a lengthy period of time and was executed in cold blood."
Det Sgt Bowen died at the scene from extensive injuries, including the loss of his left arm.
Mr Wallis, who was standing nearby, lost an eye and suffered severe burns in the blast.
He died in 2018.
Prosecutors argued the bombing was a personal attack on Sgt Bowen.
They said Perre's hostility towards him had grown because of their interactions following the seizure of a multi-million dollar cannabis crop in the Northern Territory in August 1993.
After his sentencing, Sgt Bowen's widow Jane Bowen-Sutton said the sentence had finally "given justice to our beloved Geoff and Peter Wallis".
"Although our loss is immeasurable, this outcome goes towards bringing a quiet acceptance of our tragic loss," she said.
"We hope our beloved Geoff can now rest in peace."
Genevieve Wallis, the daughter of Mr Wallis, said Perre's jail term was both justice and retribution.
"This sentence allows our families to move forward," she said.
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