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Mo Bartz, director of the county council's Information Services Group, resigned "for personal reasons" after the auditor, alerted by a whistleblower, found "significant weaknesses" in the county's IT organisation.
The district auditor highlighted problems with:
- Tendering and accounting for consultancy services
- Staff recruitment
- Management of vehicles.
The auditor questioned the use of a Buckinghamshire-based employment agency, which received £700,000 from the council from 1996-99.
Other detailed allegations made by the whistleblower could not be substantiated, the district auditor said.
Peter Davies, the new chief executive of Cornwall County Council said, "Certain procedures within the Information Services Group were found to have some significant weaknesses, and robust action has already been taken by managers to address these.
"I have discussed the findings with the district auditor and he is satisfied that there are no issues raised which are contrary to law, and there has been no willful misconduct by any employee."
Mo Bartz was unavailable for comment.