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Read more: Sturgeon defends health secretary amid calls to resign
The Herald revealed that trustees of NHS Tayside's endowment fund had agreed to release the funds in 2014 after the health board ran out of money
The health board had to temporarily suspend its constitution to allow the transfer to proceed as it breached its own rules.
Giving evidence to Holyrood's Public Audit Committee, Ms Gardner said auditors had flagged that "as being something which was an unusual transaction which played into the growing picture of financial pressures at NHS Tayside".
She said: "Internal auditors raised concerns about the retrospective transactions back in 2014 and it is included in the external auditors report as well.
"There is a significant question about why, throughout the NHS system, warnings from auditors are not being taken seriously. The reason why is something you would need to ask of Scottish Government and of the board itself."
Read more: NHS Tayside axed own rules to use charity cash to pay for IT
Sources previously told the Herald that the internal auditors from NHS Fife and Forth Valley had come under pressure from NHS Tayside executives in 2014 not to "rock the boat", with an…