Electronic patient care records will require an "enormous effort" and a "high cost" to fulfil their potential, a study warns.
University College London researchers said the project had been dogged by technology problems and tensions which had led to delays.
They said early evidence from users also suggested benefits were limited.
The new government backed e-records, but said it was right to review the way they were being rolled out.
The development of a medical records database for 50m patients in England is a central plank of the £12bn upgrade of the NHS's IT systems.
The basic patient record - known as the summary care record - includes information on allergies, medication and adverse reactions.
Further details may be added over time and it will be accessible to healthcare workers anywhere in the NHS eventually.
Problems have dogged the scheme for years with GPs raising concerns about patient confidentiality and safety.
To date, just 1.2m patients have had their records uploaded although 30m have received letters informing them about the system.
The UCL team interviewed patients and professionals involved with the project as well as analysing data from a range of sources during the research.
It found there had been difficulties over what should actually be included in the records, while ensuring GP records were complete and accurate had been a "huge task".
Transferring data had also proved problematic because of incompatible computer systems.
All this meant that extra costs in terms of staff time and financial investment were being incurred, researchers said.
This may even lead to the programme going over the £200m budget, the BBC understands.
The report was also critical of the opt-out system. Patients are allowed to stop their records being uploaded, but less than 1% of those who were written to have done this.
However, the researchers said many patients had appeared to throw away their letters before reading them.
Even where the records were available doctors were not always using them, and there had been little improvement in patient safety apart from a fall in medication errors in some cases, they said.
The hoped-for reduction in consultation length had not materialised either, the report added.
And the researchers also looked at HealthSpace, the internet site that allows patients to enter their own data and plan appointments. They said it currently had "limited functionality" and few people sign up for it.
Lead author Professor Trisha Greenhalgh said: "This research shows that the significant benefits anticipated for these programmes have, by and large, yet to be realised."
She urged the new government to have a "frank and open discussion" about the findings, before pushing ahead further with the scheme.
A Department of Health spokeswoman said: "We believe the current processes that are in place need reviewing to ensure that both the information that patients receive and the process by which they opt out are as clear and simple as possible."
Dr Laurence Buckman, of the British Medical Association's GPs committee, said the report had uncovered "some very serious issues".