Strategic health authorities could be forced to loosen ties with deaneries, after a 'bombshell' decision to class deaneries as employment agencies.
The decision by the Employment Agency standards inspectorate means deaneries have to comply with the Employment Agencies Act or face legal action from medics.
They must provide more information to junior doctors applying to training posts - for example when and where they will start, what hours they will be working, and how much they will be paid.
The British Medical Association has already reported all 15 English postgraduate deaneries to the inspectorate for breaching their duties during last year's recruitment crisis.
If deaneries aligned themselves more closely with universities - which are exempt from the legislation - in order to avoid legal action, this would weaken SHA power over recruitment.
That would be a policy U-turn as in recent years deaneries have moved away from universities and forged stronger links with SHAs.
London deanery programme director Richard Marks said: "At the moment, universities have hardly any say [in recruitment]. It's all to do with power and who's in charge.
"This is a bombshell and I don't think anyone has really thought through what the implications are."
Deaneries are ill equipped to deal with the level of red tape the change would involve, he warned.
But NHS Employers head of programmes David Grantham said although the decision had caught people "unawares" it should involve only "administrative tweaks".
One option would be to amend the legislation to treat deaneries more like universities. He advised deaneries to seek legal advice.
BMA junior doctors committee chairman Ram Moorthy called the change significant.
"It's hard to imagine another profession where you could start salaried employment without knowing how much you'll be paid in six months' time," he said. "That's been the reality for junior doctors for years, but it may be about to change."
Some trainee doctors may be able to take legal action against deaneries, for example if they lost out on pay because of a lack of information, he said.