If any boycott becomes widespread, it will mean that thousands of GPs across England will not participate in two of the biggest projects within the NHS programme: Choose and Book and the Care Records Service.
Choose and Book is one of the government's top political priorities for the NHS and has the backing of the prime minister.
By the end of next year the system is scheduled to allow millions of patients and their GPs across England to be able to book hospital appointments online from a choice of times and locations.
Local medical committees, comprising representatives of thousands of family doctors, voted in June not to engage with the Care Records Service until their concerns were addressed.
GPs are concerned that confidential information in records they hold on patients could be compromised if this data is sent to the Care Records Service. The service includes a data "spine" - a national database of patient records in summary form.
Doctors are worried that their boycott of the Care Records Service will be rendered pointless if Choose and Book systems automatically extract confidential patient data from GP systems and transfer it to the spine.
A guidance note is due to be sent to GPs by the General Practitioner's Committee of the British Medical Association, which will warn doctors to consider the implications before becoming involved in Choose and Book.
A boycott of the two main national systems within the national programme would indicate that a non-technical issue - patient confidentiality - is one of biggest risks to the programme.
If GPs were to use Choose and Book systems, they could be in breach of a decision of local medical committees not to engage with the data spine.
A spokesman for the NPfIT said, "The spine and Choose and Book have extensive controls for information governance and security." These include patient consent; two factor authentication; role-based access control, and an audit trail, he said.
"The new arrangements will be much more secure than current practice where paper records and letters are sent through the post," added the spokesman.