Civil servants are trying to amend a legal 'technicality' that grants junior doctors the same rights as employment agency workers.
The move follows an Employment Agency Standards Inspectorate statement saying deaneries appear to be classed as agencies.
The British Medical Association last week celebrated the announcement on the basis it gave junior doctors the right to demand more information about pay, working hours and when contracts start and end.
According to the BMA, the change will force deaneries to comply with laws and codes of conduct relating to employment agencies.
But the Department for Business, Enterprise and Regulatory Reform, responsible for the inspectorate, has said it is considering options, including legislation, to ensure deaneries are exempt from such rules.
A department spokeswoman said the situation arose because NHS re-organisations moved deaneries away from universities, which are exempt from work agency regulations, towards strategic health authorities.
She said: "They shouldn't be classed as employment agencies. It is just a technicality. We're working with the NHS to come to an arrangement." Deaneries should be "carrying on business as usual", she said.
NHS Employers head of programmes David Grantham said deaneries had already been advised to act as if the legislation applied to them, for example by ensuring junior doctors were given all necessary information about posts.
The change was not too burdensome as deaneries are already obliged to keep nationally agreed terms and conditions, he said.
The row has been brewing since May, after the BMA asked the inspectorate to consider whether employment agency laws applied to deaneries. It later accused the BMA of issuing "misleading" statements.