Doctors have called for a review into the £6.2bn NHS computer project, according to a survey by BBC News.
Half the GPs surveyed did not use the computer booking system
The IT upgrade aims to link up 30,000 GPs to nearly 300 hospitals in a radical overhaul of the NHS IT network.
Half of the GPs said the "choose and book" online booking system was poor or fairly poor. The poll was completed by 447 hospital doctors and 340 GPs.
And in a further blow, ministers said other parts of the project were behind schedule, pushing it over budget.
KEY PARTS OF NHS IT UPGRADE
Choose and book - A system to allow patients to book hospital appointments at a place, date and time of their convenience from GP surgeries. Nearly 10m such referrals are made each year
NHS care records service - An electronic database of patient medical records which will allow NHS staff across the country to access information wherever someone is treated
Electronic prescriptions - More than 325m prescriptions are made each year. By 2007 the paper based system will be replaced with an electronic version, which will allow patients to pick up repeat prescriptions from any pharmacy in the country
The Financial Times reported that the government had admitted the electronic records system - a database which could be accessed by health professionals anywhere in the country - was more than two years behind schedule.
Instead, the NHS has been promoting the choose and book system, which it said has helped make 400,000 appointments to date.
But in the survey, by BBC Radio 4's File on Four, doctors remained less convinced. Four out of five GPs had access to the computer system, but half said they rarely or never use it.
Only about one in five said it was good or fairly good.
The overwhelming majority - 85% - say there should be an independent review of the entire scheme by technical experts to check its basic viability.
As well as choose and book, the upgrade also involves a centralised medical records system for 50m patients, e-prescriptions and fast computer network links between NHS organisations.
Asked if the cost of the upgrade was a good use of NHS resources, almost two-thirds of GPs and hospital doctors said no.
Oxford University IT expert Professor Martyn Thomas said: "It may very well be that the programme is actually under control and they are aware of all the risks and that in due course systems will be delivered which will prove to be absolutely ideal for all the people who will need to use them.
"All I can say is it doesn't look like that at the moment."
But Dr Simon Eccles, from Connecting for Health, the organisation overseeing the IT project, said: "We have no difficulty with an independent assessment. We would welcome such a move.
"Our view is that we are already under enormous scrutiny, political financial and otherwise. We would be happy with further scrutiny, providing we don't delay the project further while answering yet more questions to explain why the project is delayed."
The poll results come as the government admitted the electronic records system could be two-and-a-half years late and cost billions of pounds more to implement.
Health Minister Lord Warner said the government had had to "regroup" over the electronic care record for all 50m NHS patients in England, which is meant to make patients' data available wherever and whenever it is needed.
The delays mean the electronic record may not be in place until early 2008 and are due partly to delays in providing the software, which is being developed by iSoft and other companies.
And Dr Hamish Meldrum, chairman of the British Medical Association's GPs committee, said there were concerns over patient confidentiality that needed to be addressed before the scheme was rolled out.
And on choose and book, Dr Meldrum added: "While the concept of being able to book their hospital appointments whilst in the GPs surgery is superficially attractive, there are a whole host of technical and practical problems that have to be addressed.
"So far, experience has been very patchy in terms of how well or badly the electronic booking system works."
And Richard Bacon, a member of the Public Accounts Committee, said the entire project had been plagued by a "whole load of problems", while choose and book was "little short of a disaster".
File on 4 investigates the new NHS computer system:
Radio 4, 2000BST Tuesday 30 May,
repeated 1700BST Sunday 4 June