Prosecutors will get a second chance at a fraud case that collapsed after nine months in court and has so far cost the financial markets watchdog nearly $3.6 million.

The High Court has rejected an application to drop charges against Viaduct Capital and Mutual Finance executives Paul Bublitz, Bruce McKay and Richard Blackwood in a case brought by the Financial Markets Authority.

The trial against the group - who ran the companies that collapsed in 2010, owing investors more than $17m - kicked off last year and was expected to last 12 weeks.

In May, nine months later, a mistrial was declared because prosecutors accidentally turned some documents over too late, breaching disclosure rules.

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Figures released under the Official Information Act show the prosecution cost the FMA $3.58m, including nearly 13,000 staff hours.

With the Crown calling for a retrial in June, the accused applied to have the case thrown out, earlier this month telling the High Court undue delay made a fair trial unfeasible.

But Justice Graham Lang this week declined to have the case stayed.

"It is entirely understandable that the prospect of a new trial would seem manifestly unfair to the defendants," he said, acknowledging already significant costs for both parties would increase.

"Without in any way seeking to undermine the significance of those factors ... they are not sufficient to warrant a stay being granted."

He said the breach by prosecutors had been inadvertent and there was no suggestion the trial was being used for inappropriate purposes.

The three executives were initially accused of a combined 49 counts of theft by a person in special relationship, along with dozens of charges of making false statements.

But as the trial went on, many of the charges were dropped.

The Crown now expects to bring 32 charges against the group in the retrial.

Charges against a fourth accused, Lance Morrison, were dropped in June, following the mistrial.

A fifth accused, Peter Chevin, was sentenced to nine months' home detention after pleading guilty at the start of last year's trial.

During that judge-alone trial, prosecutors said Strategic Finance founder Bublitz and Viaduct chief executive Nick Wevers - who died in 2014 - set up Viaduct to raise cash for their various struggling property developments.

But they didn't tell investors about the links between the companies, prosecutors said.

Bublitz' lawyers denied this, saying there was no conspiracy and the outcome was the product of proper commercial decisions in tough market conditions.