Andrew Way, chief executive of London's Royal Free Hospital, said technical problems had cost the trust £10m and meant fewer patients could be seen.
The Department of Health said lessons had been learnt from the trial.
The England scheme, part of a £12bn IT upgrade, aims to put 50 million patient records on a secure database by 2014.
The Royal Free, one of a number of early adopters of e-records, has been using the system since last summer.
The project, restricted to England, has been one of the most controversial aspects of the overall 10-year IT programme, which also involves an online booking system, digital imaging for X-rays and electronic prescriptions.
Mr Way said the cost of the problems had meant the hospital had been unable to invest in new equipment.
He also said technical glitches had caused more work for staff and meant out-patients' bookings were taking four times as long.
As a result, the hospital has had to employ another 40 administrative staff to handle the extra workload, he added.
The faulty system had also prevented the hospital from billing other parts of the NHS for treatment.
Mr Way said: "I think it is very disappointing that the work we had to do as a trust has caused our staff so much heart-ache and hard work.
"Many of the medical staff are incredibly disappointed with what we have got.
"I have personally apologised for the decision to implement the system before we were really clear about what we were going to receive.
"I had been led to believe it would all work."
However, he said he still believed in the idea of replacing paper records with an electronic system, but it would need more work to get it right.
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