Andrew Way, the chief executive of the Royal Free Hospital, said the move to electronic records had cost the hospital £10m, increased waiting times for patients and required an extra 40 admin staff.
Way told the BBC he had personally apologised to staff for taking the decision to go ahead with the project. Way said it cost £10m to implement the technology and fix it. He estimates it cost the hospital another £6m because it treated less patients and because the system failed to properly bill other parts of the NHS for work done.
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.
"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."
The Royal Free is one of the early adopters for the increasingly beleagured project. Last month the Public Accounts Committee suggested giving the scheme another six months to show some improvement or put it out of its misery.
The National Programme for IT is one of the world's largest public technology projects. It is expected to cost at least £12.7bn and is currently about four years behind schedule. Some parts of it, like digital X-rays, appear to be working but the central patient record scheme has suffered from a series of problems.
In the north of England patient records rely on Lorenzo software from iSoft - the government was forced to bail the firm out.
In the south of England the project was meant to benefit from competition between two suppliers - BT and Fujitsu - but then Fujitsu decided to end all involvement. Accenture also decided to end all involvement with the scheme.
This month BT said it was putting a number of contracts under review after announcing a big write down at its services arm. The NHS contract is thought to be high on the review list.®