Health Secretary Alex Neil has pledged to deal with NHS boards that fiddle their waiting times figures amid concerns that the practice has spread beyond just one board.
NHS Tayside has suspended two staff for suspected manipulation of waiting times figures, MSPs were told.
It comes after NHS Lothian patients who refused to travel to England for treatment were removed from an 18-week waiting list.
Labour health spokeswoman Jackie Baillie also implicated NHS Grampian and NHS Greater Glasgow and Clyde during a Labour-led debate on the NHS at Holyrood.
Mr Neil conceded "some things go wrong from time to time" in the NHS but said if the Government finds out or is told about it, he and Public Health Minister Michael Matheson will deal with it. But Ms Baillie said there is "a culture of fear and intimidation at the NHS" which compels staff to cover up malpractice.
Conservative health spokesman Jackson Carlaw joined her in demanding an apology from SNP MSPs who accused the opposition of innuendo, casting aspersions, reaching the wrong conclusions and blundering by not accepting assurances of accuracy about NHS Tayside's figures from its chairman.
Ms Baillie said: "What is now becoming clear is that the manipulation of waiting times figures was going on well beyond NHS Lothian, at NHS Tayside, NHS Grampian, and allegations have been made about NHS Greater Glasgow & Clyde. Labour members said months ago that the practice was widespread and we even gave examples, but the former Cabinet Secretary (for Health Nicola Sturgeon) was in denial. She said this was just a local problem.
"I even recall (SNP MSPs) Mark McDonald and Joe FitzPatrick accusing me of innuendo and casting aspersions about NHS Tayside. This would have of course be the same NHS Tayside that last week suspended two members of staff for suspected manipulation of waiting times."
Mr Neil said: "In dealing with the issue of the alleged fiddling of the figures, we have 14 audits going on. Every one of those reports will be published by the end of the financial year, and where there is fiddling we will deal with it.
"Unlike Labour, we will not have hidden waiting lists. We will not hide behind anyone. If there are problems to be solved, we will tackle them and we will solve them."