Six out of 14 boards, including Greater Glasgow, failed to record if doctors are being paid by drug companies. Civil servants have launched an urgent review of the oversight. Several exposes have revealed the financial links between doctors and Big Pharma.
The industry paid £38.5 million to UK doctors last year, a sum that included consultancy services and fees for attending conferences. But drug companies do not have to name the doctors who benefit until 2016.
Dr Peter Gordon, a consultant psychiatrist at NHS Forth Valley, last year lodged a petition at Holyrood calling for legislation to ensure employees declared payments. It then emerged that NHS guidance had been in place for a decade.
The 2003 circular states that, in respect of the pharma industry, boards must establish a register of interest for all NHS employees and primary care contractors. Hospital doctors are classed as NHS staff, while GPs are primary care contractors. The Scottish Government wrote to the 14 regional boards about their compliance with the guidance. The responses reveal big divergences on the section relating to GPs.
NHS Ayrshire and Arran has a system of declarations for staff, but it "does not currently extend to primary care contractors". The Borders health board also noted that it has a register for employees, but conceded it did not apply to GPs.
NHS Dumfries and Galloway gave a similar response: "In relation to primary care contractors, no comprehensive register is held at this time." The board is reviewing its procedures in this area.
NHS Greater Glasgow and Clyde, which serves 1.2 million people and has the most GPs of any board, has an online system to declare interests.
But it informed the Government: "There is not a current register of interests system which I am aware which covers GPs."
NHS Orkney said its register had no "direct reference" to primary care contractors, while the body in Shetland said GPs did not fall under its disclosure regime. Boards whose registers do cover GPs include NHS Highland and NHS Western Isles.
Each GP surgery in NHS Fife has to maintain a register of all gifts with a value greater than £100, while NHS Tayside said independent contractors were asked to complete a register and disclose hospitality.
In an article for the British Medical Journal, Glasgow GP Margaret McCartney argued the status quo was a problem: "When my doctor recommends an intervention, I don't know whether her education on my condition has come solely from a drug company representative - despite the associations between drug company education, higher prescribing costs and lower quality." The patchy compliance has prompted calls for legislation.
Dr Gordon said: "It is encouraging that a few NHS boards in Scotland appear to be fulfilling their obligations in terms of having a register of interest. It is disappointing that such progress still seems to be the exception rather than the rule."
Neil Findlay, Scottish Labour's health spokesman, said: "Clinical decisions should not be made on the basis of who makes a particular drug and the relationship a doctor has with a specific company so a register of interests makes sense."
A Scottish Government spokesman said: "The Health Secretary has asked officials to urgently investigate why some NHS boards have not put in place registers as covered by the 2003 circular. Alex Neil believes the guidance is clear that this action should have been taken, and we are looking for clarification on why some boards have not acted."