Dozens of people have been taken into custody following days of raids targeting users and suppliers of the Ghost app, including gangs allegedly responsible for drug and firearm deals.
The bulk of the arrests were in New South Wales, but alleged criminals in Victoria, Western Australia, South Australia and the ACT were also caught in the net.
Some 700 Australian Federal Police members were involved in the operation, which ran alongside an international task force targeting offshore links.
Thirty-eight people were arrested across the nation, with more expected to be charged on Wednesday.
The raids, which stemmed from a tip-off from French authorities in 2021, also took down a global encrypted communications network, investigators said.
Jay Je Yoon Jung, who police allege created and maintained the encrypted network, has been charged with numerous offences, including supporting a criminal organisation and dealing with the suspected proceeds of crime.
The 32-year-old did not apply for bail in court on Wednesday and will remain in custody before the case returns in November.
Jung allegedly distributed modified smartphones for about $A2350 ($NZ2560) , which paid for a six-month subscription to the encrypted network and tech support.
The deal also allegedly included regular software updates, which ended up being the network's downfall.
"We infected the devices, enabling us to access the content," AFP deputy commissioner Ian McCartney told reporters on Wednesday.
Jung lived with his parents and did not have a criminal history, police said.
AFP Assistant Commissioner Kirsty Schofield said arresting officers had to act quickly to prevent Jung from wiping the network before he was arrested on Tuesday.
There were about 376 of the handsets active around the nation at that point. Hundreds more were allegedly being used in Sweden, Ireland, Canada and Italy.
The police operation also prevented 50 deaths or serious injuries through infiltration of the communications networks, AFP officials said.
"On one occasion we could see over the platform an image of a person who had a firearm to their head," Ms Schofield said.
"We had an hour in which to respond to that threat," she said, adding the alleged kidnapping victim was rescued after information was passed on to local police.
The dozens of crimes that police claim to have prevented were detected since March, however it was unknown how many others were planned on the platform as it operated for close to a decade.
Encrypted communication networks, including some reliant on dedicated devices, have become a focus for law enforcement targeting transnational organised crime.
The AFP and the FBI previously ran a purportedly secure communications platform, AN0M, which criminals used to discuss murder plots, drug and weapons deals in the belief that their messages were secret.
It was exposed as being part of a law enforcement operation in 2021.
Mr McCartney said the latest operation established the agency as a world leader in cracking communication networks.
"The holy grail is always penetrating criminal platforms," he said.
Mr McCartney was confident in the strength of the cases and admissibility of evidence after past court fights over the use of information gathered through AN0M.
"We're going after the top end of town in terms of organised crime, so they're going to do everything they are entitled to in terms of challenging these matters."
