Rules on off-payroll payments were introduced in 2012 amid anger over senior public officials minimising tax liabilities by being paid through companies.

A Treasury review that year said all board members with significant financial responsibility should be on the payroll unless there were exceptional circumstances, and set out sanctions if rules were broken.

CCGs formally started work in 2013 but payroll arrangements have differed between CCGs, apparently due to confusion in particular about the status of GPs, who typically are employed by their practices, and are therefore not technically NHS employees.

There have also been complaints that official advice is unclear. Annual reporting guidance to CCGs from NHS England in 2014 about off-payroll payments to GPs said: “The role undertaken is irrelevant; it is the mechanism for paying the individual that determines whether they are on or off-payroll.”

The Healthcare Financial Management Association said in a report last year that part of the problem was there was no clear definition of an off-payroll individual.

It said it was “not enough for the individual to declare that they are self-employed or otherwise”.

“The decision has to be based on the working arrangements which are proposed,” it added.

Ellie Gamble, associate director for tax at Grant Thornton, which has issued a series of warnings to CCGs over off-payroll payments, urged commissioners to examine their positions as a priority, with particular reference to office holders.

These are generally permanent, substantive positions, not linked to the identity of the individual holding it and capable of being held by a series of people.

She said: “I would advise CCGs to be proactive, knowing that HM Revenue and Customs are likely to visit to review this. In a situation where you have got this wrong, you need to make a disclosure to HMRC before they knock on the door.”

She said NHS organisations also needed to take action following changes in the Budget due to come into force next year, which put further onus on public sector organisations in assessing the employment status of individuals paid through companies.

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CCGs risk fines and unpaid tax bills for breaking pay rules