Professor Zygmunt Krukowski was suspended from his job following an internal probe into his practices at Aberdeen Royal Infirmary (ARI) in May 2015.
His colleague Dr Wendy Craig was also under investigation but resigned shortly afterwards and is now believed to be working in the north-east of England.
Professor Krukowski, who is now retired, specialised in thyroid disorders, including cancer.
He was the Queen’s personal physician when she was in Scotland.
An investigation was launched last year by the General Medical Council after damning reports on ARI and other hospitals across the NHS Grampian region were published in December 2014.
The reports, by Healthcare Improvement Scotland and the Royal College of Surgeons, found issues in the management of the ARI which was having an impact on patient safety and care.
Low morale was also reported and the unprofessional behaviour of medical staff coupled with poor relationships between senior staff and management.
Eight doctors were investigated as part of the NHS watchdog probe and have all now been cleared.
The cost of paying the consultant salaries, legal payouts and hiring locum doctors during the investigation, which has lasted almost two years, could cost the health board at least £5 million.
A source, who did not want to be named, said: “Ultimately, this is wasting millions which should be directed towards improved patient care.
“Instead, specialities are left uncovered with procedures carried out haphazardly by those not previously practising or fully trained in areas.”
Three of the surgeons investigated by the GMC are believed to be still working at the health board although five staff, including top surgeon professor Krukowski have left NHS Grampian.
An NHS Grampian spokeswoman said: “We do not comment on the circumstances of staff or about people if they leave our employment. NHS Grampian strives to provide high quality patient care. We are confident in our general surgery team and are looking to the future, maintaining the quality of surgical services.”