Clinical waste may be left to fester at GP practices from next month unless they provide detailed information about what they are throwing away.
GP leaders warned some practices might be unaware of the requirements and could face 'major problems'.
Practices are among providers being targeted in a crackdown by the Environment Agency from 1 October.
Under the watchdog's rules, waste treatment sites that accept clinical waste must obtain detailed information about its composition before they accept it.
GP practices and other producers of clinical waste must regularly provide data on the 'quantity of waste produced; individual constituents of the waste stream; and hazards associated with the waste'.
Failure to comply could trigger 'enforcement action', and waste sites may refuse to accept the clinical waste, a briefing paper by the Environment Agency warns.
Wessex LMCs chief executive Dr Nigel Watson said: 'It could be a major problem. Any practice will generate a lot of waste, and the risk is they will be tempted to chuck clinical waste in with the general rubbish.'
Dr Watson said it appeared the rules were 'trying to crack a nut to do with a different provider', but had been applied to GP practices anyway.
'Practice managers may know about this, but it's possible practices do not,' he warned.
'It's an example of bringing something in and not thinking through the practicalities.'
The Environment Agency advice says practices may be charged a fee by their waste collector if they want them to help compile 'pre-acceptance data' about their waste.
The watchdog says practices that fear they will be unable to compile the information required should contact their waste collector.