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Local service providers contracted to the programme in deals worth billions of pounds will support and fund GPs' software from iSoft and IDX and will provide an alternative GP clinical system.
However, because Emis, which is used by more than half of GP surgeries in England, does not have a contractual relationship with local service providers, the system will have to be supported at a local level by primary care trusts.
"If primary care trusts are left to pick up the bill for practice systems, there is little doubt they will not be able to afford it without redirecting resources from patient care," said Mike Sobanja, chief executive of the NHS Alliance, a body representing primary care trusts across England.
Emis users are likely to want to stay with the system because they are familiar with it, and use it to collect data for the new General Medical Services contract, under which they are paid. Primary care trusts are obliged to support Emis under the terms of the General Medical Services contract.
Emis systems and hardware cost about £4,000 per surgery per year to support, according to Manpreet Pujara, a GP and chairman of the Emis User Group.
About 4,000 practices in England use Emis, so resources diverted from patient care could amount to £16m a year. Although local service providers would offer alternative GP systems, many Emis users would want to stay with the software, Pujara said.
Emis users feared loss of earning from moving to a new system, and said they did not have the time to retrain when existing systems suited their needs, he added.
A spokeswoman for the NPfIT said GPs could continue to use existing systems as long as they were compliant with the NHS Care Records Service. Funding for systems was covered by the General Medical Services contract and primary care trusts have allocated funding for IT.
"The national programme recognises that Emis supplies a significant number of systems to primary care practitioners, and the national programme has made efforts to encourage Emis to engage with local service providers. It is a matter for the company whether it enters into arrangements with any of the local service providers," she said.