The Crown had accused Jacob Anthonisz, 46, of conspiring with disgraced bureaucrat Paul Whyte to siphon about $22 million from public sector agencies using false invoices.
But on Friday prosecutors applied to the Supreme Court in Perth to discontinue the matter, saying WA police had not completed its investigation despite working on the case for three-and-a-half years.
Prosecutor Michael Cvetkoski said some of the work done was not of a standard that could be presented to a court and more time was needed to investigate the allegations against Mr Anthonisz.
"It is regrettable the state is not able to present a case against Mr Anthonisz at this time," he said.
Justice Joseph McGrath granted the application but said it was "a most unsatisfactory outcome".
"It is deeply regrettable that we are in the position," he said.
"The authorities have been investigating and preparing for trial for a substantial period of time.
"The accused is entitled to a timely trial and he must now wait another 18 months.
"With regret, I vacate the trial that was to commence on 24 July."
Mr Anthonisz was charged with 542 corruption offences in December 2019 after police alleged he had been involved in a similar number of financial transactions using dozens of bank accounts over 11 years.
In summarising the Crown's position, Justice McGrath said there had been a breakdown in communications between prosecutors and police over the years, and a lack of continuity in the police investigation team.
He also said Mr Anthonisz was no longer subject to any allegations or bail and was "free to go ... You re-enter the community as a person not subject to any sanctions".
However, the court heard prosecutors may recommence proceedings over same alleged offences when police complete their investigation.
Mr Anthonisz's lawyer, Simon Freitag, said his client was relieved and frustrated for the charges to be dropped.
"It's been a burden on him and his family for all of that time," he said.
"It's affected every aspect of his life."
He said Mr Anthonisz maintained his position of not guilty.
He also said he may make abuse of process objections or an application for a permanent stay of proceedings if Mr Anthonisz was charged again.
Whyte is serving a 12-year prison sentence after he admitted masterminding what local authorities have described as Australia's biggest corruption by a public servant.
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