Scientists have forced the government to back down from its controversial plans to control the use of tissue taken from patients during operations.

Doctors had warned that new legislation - introduced in the wake of the Alder Hey organ scandal on Merseyside - would cripple vital research.

Among the projects threatened by the Human Tissue Bill, which receives its third reading next week, is the recently launched National Anonymous Tonsil Archive which was intended to collect 100,000 samples, removed during routine operations, in order to discover the extent of the brain disease, CJD, in Britain.

The archive's director, Professor Noel Gill, recently warned civil servants there was a danger that the project would have to be abandoned if the bill was enacted as it stands. 'There would be significant problems for us proceeding with our work,' he told The Observer .

According to the original bill, it would become a criminal offence, punishable by prison, for a doctor to use any leftover material - even a urine sample - from a living patient for research without getting the patient's consent.

A patient would have to sign a specific form to give approval for researchers to use his or her tissue - such as a set of tonsils. At present, no such consent is needed.

'Surgeons carrying out operations would have little time and might not understand the issues involved in a research project that has nothing to do with their field of medicine. But they would still be supposed to counsel patients about filling in consent forms,' warned pathologist Peter Furness, from Leicester General Hospital.

'Pilot studies have proved it won't work. Supplies of tonsils and other tissues will dry up. The alternative - to use organs or tissue without consent - could land researchers and doctors in jail. Schemes like the tonsil bank will become impossible. This bill would create an offence where no one has been harmed, no one has complained, and the 'criminal' was just trying to improve medical care.'

These criticisms were backed by leading scientists, including the head of the Royal Society, Sir Robert May, Mark Wolport, head of the Wellcome Trust, and the British Medical Association. Sir David King, the government's chief scientist, also agreed with the critics.

As a result of this intense pressure, ministers are expected to water down the bill when it comes back to parliament. 'The trick for us is making sure that it's not so burdensome that science comes to a halt, but that patients know what is going on,' said a Department of Health source. 'We are broadly sympathetic on this.' However, the official added that researchers would not be allowed to do exactly what they wanted.

At Alder Hey organs were removed from dead children without their parents' knowledge and stored for research. The families only found out the bodies had not been buried whole - crucial for some religious faiths - years later. But scientists say the current legislation confuses samples taken from living individuals with organs removed from the dead.

Rosie Winterton, the Junior Health Minister, is not expected to back down on the bill's requirements for deceased patients, which would force doctors to ask relatives before taking organs. But she is expected to publish amendments covering the requirements for live patients, who undergo operations or medical procedures and leave so-called 'residual tissue' - removed organs, or slides of tissue or blood - which would otherwise be destroyed.

The details of the changes are still being drawn up, with amendments likely to be published next week. But Ian Gibson, chair of the Commons Science and Technology Select Committee, welcomed the retreat. 'All we have been hearing from the scientific circuit is "this bill is dreadful",' he said. 'At last they have got their act together.The idea that each time you take a urine sample you should be asking for consent - how anybody thought that could happen I don't know.'