The hospital doctors, employed by NHS Lothian, have been carrying out work which the board farmed out to a private hospital.
The health board used Murrayfield hospital, owned by Spire Healthcare, to hit waiting list targets.
NHS Lothian paid Spire Healthcare £3.2 million a year, in a three -year contract starting in 2008.
But the company used many of the same consultants as the health board to treat these patients.
The Scottish Liberal Democrats are now calling for Health Secretary Nicola Sturgeon to make a statement before parliament on the matter.
The hospital medics, who earned up to £100,000 from their NHS work, were paid for more work by Spire.
New figures show 64 consultants worked for the NHS and Spire in 2010.
This included 18 orthopeadics specialists, 15 specialising in endoscopy and 12 in general surgery.
In 2011, nearly 80 consultants worked for the health board as well as the company.
An internal audit by NHS Lothian found a number of concerns about Spire.
It said there were potential “conflicts of interest” where “consultants and other staff employed by NHS Lothian can benefit from
treating NHS Lothian patients privately.”
The report found it cost “significantly more” to pay Spire than treat the NHS patients in-house.
Some consultants had set up special firms to handle referrals to Spire.
Though the contract ended last year, NHS Lothian continues to send patients to Murrayfield hospital.
Dr David Farquharson, NHS Lothian’s medical director, said: “When we deal with a private provider… we are working with that company and not liaising with individual consultants who may or may not also work in Lothian.”
Scottish Lib Dem leader Willie Rennie said: In November last year the First Minister claimed that he had “eradicated the private sector”
“These figures prove him optherwise.”
A BMA Scotland spokeswoman said: “The 2004 Consultant Contract clearly sets out an individual consultant’s obligations to the NHS… the contract specifies that they must either offer to work an additional programmed activity for the NHS or they may forego their pay progression.”
Figures released last week showed than 7,000 patients were left too long on hospital waiting lists at NHS Lothian.
Despite £5million being pumped into NHS Lothian to clear the backlog of patients, the waiting list figure continued to rise.
The health board now says it will not meet a target to get the waiting lists under control by June.
Practices of manipulating waiting list figures were stopped in October.
Auditors said staff complained of an “atmosphere of fear” in the health board and a “bullying culture.”