Some senior NHS staff believe that continuing delays in the NHS IT programme could risk patient safety.
Current systems are out of date
Interviews with managers at a small number of hospital trusts also revealed financial deficits were hampering the £12 billion project.
NHS IT bosses have strongly denied that patient safety could be affected.
The scheme - the world's biggest civilian IT project - aims to allow full electronic booking across the NHS and centrally-held patient records.
However, it has been dogged by criticism throughout, and hit by substantial delays.
The NHS-funded independent research project was carried out by King's College and Imperial College in London, the London School of Hygiene and Tropical Medicine, and the University of Bristol and published by the British Medical Journal.
It found some staff thought that having to rely on elderly systems was bad for patients.
One medical director told the researchers: "Our path (pathology) system is extremely out of date, it's not just obsolescent, it's obsolete.
"When we had to buy some new bits for it recently we had to buy them through eBay from someone in America because there's just no bits in this country, so it's a huge risk to the trust."
Lead author Professor Naomi Fulop of the School of Social Science and Public Policy at King's College London comments: "While the delays continue, IT networks are becoming outdated and there is a real risk that patient care could be compromised."
However, the bulk of the concerns voiced by those interviewed were about 'poor communication' between Connecting for Health - the NHS body tasked with delivering the new systems - and trusts, and about the impact of financial deficits on the project.
Some of those quoted in the report were scathing about both the concept and the delivery of the flagship 'Choose and Book' systems, which should allow patients to choose their hospital at the touch of a button in their GP surgery.
The researchers did find, however, that support for the aims of the NHS IT programme remained strong.
Another researcher, Dr Barney Reeves of the Clinical Trials and Evaluation Unit at the University of Bristol added: "It will be a disaster if the opportunities afforded by the programme are jeopardised by the challenges associated with implementation."
However, Dr Simon Eccles, Connecting for Health National Clinical Lead, said that while progress had been slow in some hospitals, those with the greatest need for new systems were being prioritised.
"It is untrue to suggest patient safety is being compromised. "This research reveals some of the challenges and frustrations of introducing new IT into the hospital sector.
"We work with those challenges every day and are working hard in partnership with local NHS organisations to overcome them to make best use of these technologies."