Mrs Bottomley- now at the heritage department - was giving evidence on behalf of the Daily Mirror, which is fighting a libel action brought by Anthony Percy, consultant orthopaedic surgeon at Queen Mary's Hospital, Sidcup, Kent.
Mr Percy claims Mrs Bottomley called for his role in the affair to be "flagged up" after she had heard that he was to be censured.
Mr Percy, 55, Bickley, Kent, says the newspaper suggested he was guilty of gross dereliction of duty, and bore some responsibility for the death of 45-year-old Malcolm Murray.
Mr Murray, who had a serious brain injury, died at Leeds General Infirmary last March after being flown 200 miles from Queen Mary's when no neurosurgical bed could be found for him in the South-east.
The newspaper, which denies libel, says its story was a fair and accurate account of the contents of the South Thames Regional Health Authority report that criticised Mr Percy for giving advice to a junior doctor from home by phone rather than going into the hospital.
Mr Percy has claimed he was set up as the scapegoat by Mrs Bottomley, the STRHA chairman, William Wells, the hospital's chief executive, Stephen Collinson, and a civil servant at the Department of Health named Hollebon.