Thousands of dollars of public money has gone missing - and Labour wants to know why the Transport Minister thought it was acceptable to not tell the people who's money it is.

The Ministry has today confirmed its general manager of organisational development was stood down over allegations of fraud last week.

It's alleged Jo Harrison used false contracting arrangements to steal about $750,000 to a million dollars.

Jo Harrison has now reportedly skipped town - and is possibly in Canada.

Ministry management was reportedly alerted to the financial discrepancies earlier this year.

Labour's transport spokesperson Sue Moroney said the public deserves to know about this.

"It's one of the top five positions in the whole Ministry, so this is serious fraud at the highest levels within the Ministry of Transport."

Moroney said it's "already in the hands of the Serious Fraud Office, so obviously the Minister would have been well briefed before that occurred."

Harrison had worked at the Ministry for several years and had been seen as a leader within the organisation.

Ministry chief Peter Mersi said an investigation has begun.

He said the Ministry's focus is on ensuring she's held fully to account for her actions - and to recover any money which may have been misappropriated.

“I cannot say more at this stage because of the ongoing investigation by the Serious Fraud Office.

“In light of what has happened, it is prudent to confirm that our systems, processes and controls are robust. To provide this assurance, a number of reviews are now underway. These focus on internal controls and recruitment processes.

“This was a senior staff member in a position of high trust, and my staff feel incredibly let down and betrayed by her actions.”

Minister of Transport Simon Bridges has been contacted for comment.