GPC Wales chairman Dr David Bailey said Welsh practices with patients living in England may need to link to the consortia across the border which will fund their care.
Around 14,000 people in Wales are registered with GPs in England, and 19,000 people from England are registered with GPs in Wales.
'Nobody in government has been able to explain what happens to practices in Wales with patients who live in England,' said Dr Bailey.
'Will their treatment be funded by a Welsh primary care organisation? Probably not, and if it is funded by consortia in England then they are going to want dialogue with those practices,' he said.
He warned that the removal of practice boundaries could create funding problems around large cities. 'There will be a similar situation wherever large numbers of patients are treated in the city they work in.'
Dr Bailey said the conference of Welsh LMCs on 26 March would discuss how England's Health Bill will affect practices near the border.
A Welsh government spokesman said health minister Edwina Hart had raised the issue with England's health secretary Andrew Lansley.
'Discussions are taking place with GPs to ensure that as the details of the changes to the systems in England emerge, we adapt the existing agreements and protocols,' he added.
The Welsh LMCs conference will also look at GPs working in 'localities' to influence services, said Dr Bailey.