Britain's doctors have today heard calls to withdraw all cooperation from the £12.4 billion UK National Health Service National Programme for IT (NPfIT).

Doctors vented their anger over the huge NHS computer project at the British Medical Association's (BMA) annual conference in Torquay, where a key resolution on the agenda warns that NPfIT is "doomed to fail".

The BMA is discussing calls for a public inquiry into the scheme, with concerns centring particularly on its cost and data security of the planned national electronic care record system.

Doctors have raised repeated concerns about patient consent and the security of records to be held on a national data "spine".

Resolutions to the BMA conference warn that the national care record system "seriously endangers patient confidentiality".

The BMA conference will also hear heavy criticism of the Choose and Book IT system for booking hospital outpatient appointments. A key resolution claims the system is "unfit for purpose" and "actually limits patient choice" – the government policy it was designed to support.

Uptake of Choose and Book by GPs is still limited, with NHS figures published in April showing that just 37% of referrals to outpatients departments went through the system – far short of the Department of Health's 90% target. But the government is piloting a scheme that would give patients direct access to the system.

A survey by specialist medical polling organisation Medix www.medix-uk.com in November found that among GPs who used the system regularly, 90% said it increased the time taken to refer a patient to hospital while 70% said it was either detrimental to patient care or made no difference.

The conference resolution describes Choose and Book as a "politically driven initiative" to reduce hospital deficits and give the illusion that government targets are being met. The IT system "should be suspended until such time as the system is efficient and effective," the resolution says.

Opening the conference, acting BMA chair Dr Sam Everington said NPfIT was in "a sorry state".

"Estimated costs of upward of £20 billion, interminable delays, the chaotic shambles that is Choose and Book, growing concerns about patient confidentiality and security – it's a wonderful exercise in how not to do things," he said.

Delivery of software for the care record system is running more than two years late in three out of five NPfIT regions, where troubled software firm iSoft is supposed to provide its Lorenzo system. Lead contractor CSC has now stepped in to manage delivery of Lorenzo and other iSoft products to be provided for NPfIT.

Questions have also been raised over the NPfIT contracts by NHS IT chief Richard Granger, who has suggested that contractors might seek changes to contracts or compensation when he leaves his post – an idea suppliers rejected. Granger is set to quit as head of Connecting for Health, the body that runs NPfIT, before the end of the year.