The 32-year-old man was arrested by federal police in western Sydney on Tuesday. He appeared in court on Wednesday charged with five offences relating to running the Ghost messaging platform which police alleged was used by several gangs and organised crime syndicates in the Middle East, Australia and South Korea to import drugs and order killings.
"Taking down dedicated encrypted communication devices takes significant skill," said Australian Federal Police Deputy Commissioner Ian McCartney. "But the holy grail is always penetrating criminal platforms to access evidence."
It was the first time for a person based in Australia to be accused of creating and running a global criminal platform, the police said.
Police conducted raids over two days in four Australian states and territories this month, with related searches also taking place in Ireland, Italy, Sweden and Canada.
Up to 50 alleged Australian offenders accused of using Ghost are also facing charges, including significant prison sentences, with more arrests in Australia and overseas likely in the next few days, police said.
Police said they had been able to prevent the death or serious injury of 50 individuals in Australia as a result of cracking Ghost's encryption.