The boss of Melbourne's major children's hospital is suing the Victorian health department secretary for blocking her reappointment.

Royal Children's Hospital chief executive Bernadette McDonald has launched a bid for the Supreme Court to overturn a decision not to renew her contract.

Ms McDonald, whose three-year term in the role expires on September 13, argues she was not granted procedural fairness

Her statement of claim, prepared by law firm Maurice Blackburn, states the hospital's board voted unanimously to reappoint her in late February.

Chair Rowena Coutts formally wrote to Department of Health secretary Euan Wallace in mid-March to approve her reappointment, but months passed without a response.

On July 2, Ms Coutts met with the department's deputy secretary and was told Mr Wallace had decided not to approve the request and to go to "market" through a "recruitment process".

According to the document, she was told "the secretary had indicated that he would not approve the reappointment of Ms McDonald as CEO even if she was identified as the preferred candidate".

A second letter to the secretary to approve the board's appointment on July 23 was knocked back two days later.

"At no time prior to the decision had the secretary or other official of the Department of Health raised concerns about Ms McDonald's ability to fulfil the role of CEO with the chair of the board or with Ms McDonald," the document said.

Ms McDonald wants the secretary's decision not to approve her reappointment quashed, or a declaration that it was invalid.

Otherwise she is seeking an injunction requiring the secretary to take steps to "dispel a reasonable apprehension of bias".

Health Minister Mary-Anne Thomas said she had been advised of the legal action but refused to comment further.

"It is a matter now that is before the courts," she told reporters at state parliament on Wednesday.