National Museums Scotland (NMS) has called in the police after an audit revealed that more than £80,000 was missing from its accounts.

The organisation asked its internal auditor KPMG to “review the integrity of certain cash withdrawals” after discrepancies dating back several years came to light last July, according to the NMS’s 2011-12 annual report.

The inquiry found that fraudulent activity had taken place, and NMS contacted the police, who have confirmed that they are investigating a report of “historic fraud”.

NMS suspended two members of staff in its financial department at the start of the inquiry. One has since been sacked and the other has resigned.

In the organisation’s annual report, the auditor said its initial findings did not “imply a fundamental weakness in the system of internal controls”.

The alleged fraud has attracted comment from political leaders in Scotland.

Willie Rennie, head of the Scottish Liberal Democrats, told The Scotsman: “The allegations of historic fraud are clearly very serious.

“I know that management at NMS will be anxious to get to the bottom of this, and it is right that the legal process is allowed to run its course.

“When it comes to bodies and organisations in receipt of public support, ministers need to be aware of exactly how taxpayers’ money is being spent.”

The police investigation is ongoing.