The health board had commissioned PricewaterhouseCoopers to carry out the work independently, initially with the agreement of Health Minister Nicola Sturgeon.
But despite work already being under way, the government has now insisted that it instructs the investigation and receives the report first.
That has now led NHS Lothian chairman Charles Winstanley to fire off a letter to Ms Sturgeon suggesting that the “integrity” of the board had been called into question.
The probe was ordered after it was found that NHS Lothian had been offering patients unrealistic appointments for elective surgery in England, and removing them from waiting list figures when they refused.
Ms Sturgeon demanded the control of the audit to be handed over to Holyrood last month in “the interests of appropriate corporate governance”.
As a result, NHS Lothian had to terminate its contract with PwC and has paid £25,000 for the work the consultants had already carried out.
Dr Winstanley agreed to the change, but told Ms Sturgeon: “Board members have asked me to relay to you their disappointment at the suggestion in your letter that their independent external audit lacked the ‘appropriate corporate governance’.
“Board members particularly wished me to communicate to you that they believe they were appointed by you in the expectation that they would act with integrity at all times”.
Dr Winstanley today told the Evening News that NHS Lothian had been first asked by the government to carry out an internal audit of waiting times processes. He said: “We have now been requested by the Scottish Government to cease that audit. I understand the Scottish Government now wants to instruct its own audit.
“As a result of that the audit committee has halted the audit and ceased all work with the auditors appointed. We will again engage as supportively and comprehensively with any new audit as we had been doing with the one previously commissioned by the board.”
A Scottish Government spokeswoman said PwC would continue its work, but report to Ms Sturgeon’s office instead
She said: “In the interests of appropriate corporate governance, the Scottish Government will take over the management of the external audit report. This will preserve the independent status of the audit function.”