UK doctors working for charities overseas are being removed from the lists of approved practitioners in the UK in their absence.
Dr Duncan has been working in Afghanistan
This means they cannot work as soon as they return to the UK.
Writing in the British Medical Journal, Dr Alex Duncan said the problem was that the doctors were unable to attend face to face appraisal.
A Department of Health spokesman said the merits of approved lists of doctors was currently under review.
Dr Duncan, a GP from West Sussex, is currently running a community health programme in the remote Great Pamir mountains in north east Afghanistan.
He said he had been removed from his primary care trust's list of doctors licensed to practise in the area in his absence.
"They were very nice and tried to see whether there was any way of getting round it but to no avail.
"This means that I cannot do locum work when I am on short leave in the UK.
"It's a nice source of extra income and a good way of staying in touch with UK practice.
"It also means that when I return to the UK I will have to reapply to the trust, a process that takes up to two months."
In an open letter to the Chief Medical Officer for England Professor Sir Liam Donaldson, Dr Duncan said overseas working gave doctors valuable experience that benefited the NHS when they returned to the UK.
However, he warned that the need for appraisal and regulation might make a stint of working overseas too difficult for doctors to contemplate.
This would be a shame, as it would deprive parts of the developing world of badly needed expertise and the NHS of valuable experience on the doctors' return, he said.
Dr Duncan called for the establishment of a body to regulate doctors who commit to working overseas for more than a year with a recognised charity or medical organisation, but who have a clear intention to return to work in the NHS.
He said this body should ensure that doctors are fit to practise in the UK at the time they depart for work overseas and at any time they return to the UK.
Dr Duncan said: "At the moment it's all a bit of a fudge. Those who are supposed to regulate me know little about my work and have no idea about the difficulties of my working conditions."
He said a regulatory authority for doctors working overseas would have the experience to know what is going on and to spot problems that primary care and hospital trusts might miss.
The system would also provide greater transparency for doctors getting back into UK practice.
A Department of Health spokesman said: "Following the introduction of the GP Register in April this year we will be exploring whether the performer list system is needed to ensure public protection and if the system is to be retained, whether it can be simplified and where appropriate made more flexible to take account of the varied career paths of modern GPs.
"It is important that all doctors keep their skills and knowledge up to date and are regularly appraised.
"We recognise the difficulties that doctors not working in managed environments face, and this will be one of the matters we will need to consider when deciding how to take forward the recommendations made by the chief medical officer in his report, Good doctors, safer patients."
The public consultation on this report, which argues for a thorough reform of doctors' regulation, ends on 10 November 2006.