The defence bid arose because of issues around the disclosure of documents.
Justice Mark Woolford has not released his full decision on why he aborted the trial but in a short ruling said he had "given the matter anxious consideration".
"Because of the admitted breaches of the Criminal Disclosure Act and the stage of the trial at which those breaches are sought to be remedied, together with the impact on the rights of the defendants to present an effective defence, I have decided that I should declare a mistrial and abort the trial," the judge said.
"If the breaches were known and were sought to be addressed before trial or even within the first three months of trial, in my view, they could have been remedied without major impact on the defendants' rights to present an effective defence. However, the breaches only became known after the Crown closed its case and the evidence for Mr Bublitz was ending in late March," he said.
The judge had already refused two applications to stay the case or dismiss charges.
"When I refused the first application last year, which was largely based on delays to date and the likely length of trial, I commented that it would be unnecessarily burdensome on all concerned if the trial continued to May or June this year. It is now mid-May and there is still no end in sight," Justice Woolford said.
Bublitz, according to prosecutors when the trial began, allegedly used the two finance companies to support his property investments. The other defendants in the case were accused of helping him. All four deny the allegations against them.
The Herald understands it is now up to the Crown and the FMA on whether they push for a re-trial.
An FMA spokesman said the authority was considering the judgment.
The Viaduct and Mutual trial was the last of the FMA's finance company prosecutions.
A fifth defendant who was associated with Mutual, Peter Chevin, pleaded guilty to nine charges of theft by a person in a special relationship before the trial began and was sentenced to nine months home detention in March.