The benefits of the £6.8bn upgrade of the NHS IT system risk being overlooked amid the criticisms, experts say.
There are fears the system will not be secure
The 10-year IT programme is aimed at linking more than 30,000 GPs in England to nearly 300 hospitals by 2014 and includes electronic medical records.
Critics have raised concerns over patient confidentiality and delays which could cause costs to spiral.
But drug regulators, NHS managers and academics said the project will improve patient safety and aid research.
The project, overseen by a government agency called Connecting for Health, is the biggest civil IT scheme in the world.
As well as setting up a centralised medical records system for 50m patients in England, it involves an online booking system, e-prescriptions and fast computer network links between NHS organisations.
GPs have raised concerns about patient confidentiality - medical records will be able to be accessed across the country although safeguards restricting access depending on a person's position are being built in.
Parts of the scheme are also running behind schedule, prompting fears the project could run over budget.
Dr Mark Walport, director of the Wellcome Trust, said he could understand the criticisms.
But he warned: "The benefits have become obscured by the focus so far. This has to be redressed."
Andrew Haw, a member of the British Computer Society and IT director at the University Hospital Birmingham, said electronic medical records would be more secure than the current paper-based approach, while most of the extra costs caused by delays would be covered by the suppliers.
He said it would help improve communication between hospitals and GPs, while digital x-rays would improve patient safety as it was often left to patients to transport x-rays from department to department in hospitals.
"There is some reluctance, but I think once clinicians realise using modern information systems reduce these... they will be convinced."
Dr John Parkinson, of the drugs regulator the Medicines and Healthcare Products Regulatory Agency, said the upgrade had the potential to improve the transfer of information on drug side effects.
He said the current yellow card system was predominantly a "passive system" requiring doctors to report problems, whereas with electronic records there would be a more comprehensive database.
"It will make a dramatic difference."
And Professor Carol Dezatuex, a Medical Research Council expert on child health, said having an electronic medical database could help with research.
She used the example of the scare over the link between autism and the MMR jab.
She said one of the most compelling pieces of evidence disproving the link came from Denmark.
"Researchers had access to a national immunisation register, autism register and birth register. It allowed analysis in a year to reassure the public."
She added having access to anonymised records helped "improve the science".
Richard Vautrey, of the British Medical Association's GPs committee, said: "It is true we have some concerns, but we also recognise there are huge potential benefits for research and for patient safety.
"We just want to make sure we get this right."