A year-long inquiry into a hospital trust that conducted an experimental treatment on premature babies has concluded that the parents were misled about what was being done to their children.

Some parents have claimed signatures on consent forms for the treatment, involving a new type of ventilator, were forged and both the General Medical Council (GMC) and the police have launched their own investigations.

Ministers are bracing themselves for the highly critical report, to be published today, into the North Staffordshire Hospital Trust in Stoke-on-Trent. After the Bristol baby hearts scandal highlighted clinical failings in the NHS, the inquiry, first disclosed by The Independent last year, is expected to call for tough new rules governing research.

Of 122 babies given the new treatment between 1989 and 1993, 43 died or were brain damaged, compared with 32 who died or were brain damaged in a control group of 122 given conventional treatment. The death rate in the experimental group was 33 per cent higher, but because of the small number of babies in the trial the difference was not statistically significant.

The inquiry, by Professor Rod Griffiths, director of public health for the West Midlands, was ordered by ministers in February 1999 after parents complained they had never been told the treatment was experimental.

They submitted a 1,600-page dossier to the GMC and the police launched a criminal investigation. These inquiries have been put on hold pending publication of the 50-page Griffiths report.

One parent said: "Everything that could have been done wrong was done wrong."

The doctors at the centre of the investigation, Professor David Southall, professor of paediatrics at Keele University and a consultant at the North Staffordshire Hospital trust, and Martin Samuels, a consultant paediatrician at the trust who specialises in the detection of child abuse, were suspended last December over separate allegations that they had "harassed" and "threatened" parents in relation to their child protection work.

However, the criticisms in the Griffiths inquiry, which was widened to include the child protection work, are expected to range beyond the two doctors and implicate other members of the hospital's staff. In apparent anticipation of the inquiry's criticisms, the trust has set up a working party to produce its own guidelines on clinical research and obtaining consent.

Professor Southall is a controversial figure who pioneered the use of covert video surveillance to identify children at risk of child abuse. Although the method proved successful, and led to 34 convictions between 1986 and 1994, it incensed parents who complained they had been wrongly accused ofMunchausen's by Proxy, the attention-seeking disorder in which parents harm their children to get medical treatment.

The allegations of harassment of parents are the subject of a separate internal inquiry, which was later split into three strands looking at employment issues, child protection and research.

Last October, Professor Southall announced that he had been cleared of allegations in relation to employment issues. In a 3,500-word statement put out by the British Medical Association, which has supported him throughout, he hit back at the "orchestrated campaign" to discredit him, accusing campaigners of seriously interfering with his work.

He said he had been repeatedly threatened, his charity for children in Bosnia had been infiltrated and burgled and research grants and international aid had been blocked. He wrote of the "immense strain" on him personally and the threat it posed to children at risk.

Two months later, on 9 December, he and his colleague Martin Samuels were suspended by the trust. Although there is normally a six-week deadline for charges to be presented to a suspended doctor none has yet been made against Professor Southall and Dr Samuels, almost five months after they were suspended on full pay. A spokesman for the trust said: "The issues in this case are so complex and so convoluted it does take time."