Dr Nigel Ostrowski is being investigated by NHS Counter Fraud Services over the alleged overpayments made by NHS Lothian.
Mr Ostrowski, who qualified with a degree in medicine from Dundee University in 1977, has also been suspended by the General Medical Council.
It is understood the former anaesthetist has quit his post at Bangholm Medical Centre in Edinburgh. NHS Counter Fraud Services yesterday confirmed there was an ongoing investigation into Dr Ostrowski.
GPs receive incentive payments for carrying out certain services under an aspect of their contracts known as quality and outcomes framework.
NHS Lothian's finances and resources committee has agreed it will be possible to pursue Dr Ostrowski personally for the alleged overpayment rather than his former practice.
A spokesman for NHS Counter Fraud Services said: "We can confirm there is an ongoing investigation. We have no further comment at this time."
Susan Goldsmith, NHS Lothian's finance director, said: "NHS Lothian takes any allegations of fraud extremely seriously. We are assisting NHS Counter Fraud Services with their investigations into this matter and as this is an ongoing inquiry we cannot comment further."
Approached at his home in the upmarket Prestonfield area of Edinburgh, Dr Ostrowski said he had no comment to make.
Neighbours said they were shocked by the allegations.
One, who asked not to be named, said: "There's been no lavish parties or fancy expensive cars around their house since I've been here anyway. He just doesn't seem the type."
A spokeswoman for the GMC confirmed the doctor had been suspended for 18 months in October last year.
Bangholm Medical Centre declined to comment.
It was revealed earlier this year NHS Scotland had been defrauded out of £2.2 million since 2008. Eight out of the 10 incidents involved NHS workers, with half escaping prosecution.
The biggest case involved an unnamed NHS employee who earned £125,066 after he "made falsehoods on a job application form in order to secure employment with the NHS." Another case involved an anaesthetic assistant who sold surgical equipment from Glasgow hospitals on eBay.