Myki's fare evasion enforcement is unfair and costly, targets society's most vulnerable and wastes countless hours on failed court cases, a Victorian Ombudsman's investigation has found.

'Overwhelming' evidence of the system's failures were unearthed by the Ombudsman despite Public Transport Victoria and the Department of Economic Development, Jobs, Transport and Resources failing to co-operate with the investigation.

Ombudsman Deborah Glass noted that she used her office's coercive powers to inspect PTV board minutes for the first time after the authority provided inadequate information, while the department took two months to provide information that was requested to be provided within 14 days.

"The issues in obtaining documents from both the department and PTV put my investigation six to eight weeks behind schedule and has delayed my tabling this report in the Parliament," Ms Glass wrote.