A man acquitted of sex charges is back in court, now fighting to recoup some of the cost of clearing his name.

The man, in his 50s, had his name, place of work, occupation and family details suppressed through the trial and that order was made permanent when he was acquitted in the Dunedin District Court in April last year.

A jury found him not guilty on all charges: five of indecently assaulting three young girls and three of trying to make intimate visual recordings of two of them.

Yesterday, the defendant sought costs for the ''significant'' funds it took to fight the Crown charges.

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While he would not be drawn on a specific figure, Jonathan Eaton, QC cited other cases where six-figure payments had been ordered for defendants who had been exonerated.

He was highly critical of the prosecution case, which he said featured ''false allegations, poorly investigated''.

''With all three complainants, the evidence at trial just became such a mess,'' he said.

The police's investigation leading up to the trial turned up no corroboration for the claims of sexual impropriety, Eaton said, and in some cases Crown witnesses give evidence that weakened the case.

''It had all the hallmarks of an investigation lacking independence and objectivity,'' he said.

Eaton highlighted the fact prosecutors never went back to the complainants after their original statements were made. Had they done so, and informed them their claims had been unsubstantiated, they might have withdrawn their complaints.

''They never got that chance.''

Eaton argued the story of the third girl, who came forward in 2016, was ''bizarre, incredible''. Had her complaint stood alone, the matter would surely never have resulted in charges being laid, he said.

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Crown prosecutor Robin Bates denied that and opposed the application for costs, saying the defence's submissions on the shortcomings of the prosecution's case were ''exaggerated''.

''Another jury could have easily convicted this applicant,'' he said.

Bates told Judge Kevin Phillips, who heard the trial last year, that while there might have been issues with the girls' evidence, the core allegations endured.

''Time, circumstance and physical opportunity'' were all substantiated at trial, he said.

Bates also stressed it took the jury at least five hours to return the not-guilty verdicts.

''It wasn't a case of dismissing these complainants out of hand.''

Had the Crown case been so deficient, Eaton should have applied to have the charges dismissed at the close of the case, he said.

Judge Phillips agreed, but that was no bar to an award of costs.

He reserved his decision.

There were few applications like this, Eaton said, because most defendants were funded by legal aid.