The DoH said the pilot will run for a year and outlined that GP practices will join the scheme on a voluntary basis only.
The three areas have been chosen to pilot the scheme as they have high numbers of commuters travelling into the area each day, the DoH said.
It added that the funding to pay for patients who use practices on a consultation-only basis will be capped at £2m, although it did not say who would be foot the bill once the funding has run out
Health secretary Andrew Lansley said the pilot is the start of a series of measures that will be introduced to make the NHS more patient focused.
He said: ‘Many patients are happy with their local GP practice, but a significant minority have problems registering with a practice of their choice. This pilot will mean patients taking part can access the high quality care they deserve in a place and at a time that suits them.
'That’s why I believe patients should have the freedom to choose a GP practice that suits their lives, and not be restricted by geographical boundaries.’