The 28-year-old alleged organiser of the attacks was arrested during a police raid at Bendigo on Friday and taken into custody.
He faces charges of sabotage, unauthorised access to computer data, and dishonestly obtaining or dealing with personal financial information - that could see him face up to 25 years in prison if ultimately convicted.
A 27-year-old was arrested in the same raid and charged with three firearms offences. He was granted bail and will appear in court in August.
Neither man has been named.
AFP acting Commander Cybercrime Operations, Chris Goldsmid said the seriousness of the alleged offending cannot be overstated.
"Each occasion a police phone line was unavailable as a result of these malicious attacks meant members of the public were unable to access a vital service. This had serious implications for the broader community," Acting Commander Goldsmid said.
"Some of the attacks included a spate of text messages asking for emergency assistance. People who called the number back reported being verbally abused by a recording on the other end. This created fear, distress and anxiety amongst some of the most vulnerable in our community."