Professor Gianni Angelini told a disciplinary hearing of the General Medical Council that he had spent more than a year before the 1995 operation trying to raise the alarm over an "unacceptable" death rate among babies undergoing "switch" heart surgery to correct a back-to-front heart at the Bristol Royal Infirmary.
Heart surgeons James Wisheart and Janardan Dhasmana are appearing before the GMC's professional conduct committee on allegations that they continued to perform operations at Bristol although they knew that at least twice as many babies died in their care than at other hospitals.
It is alleged that they went ahead with operations which led to the deaths of 29 children between 1988 and 1995, and left four others brain dead.
Dr John Roylance, former chief executive of the United Bristol Healthcare Trust, is accused of allowing the two surgeons to continue operating. All three men deny charges of serious professional misconduct.
Professor Angelini told the hearing that he was first alerted to problems with the switch operations in autumn 1993, when he received data showing an alarmingly high death rate."My view was that we were no good at these operations, end of story," he said.
Professor Angelini said he begged Dr Roylance and Mr Wisheart not to allow an operation on 18-month-old Joshua Loveday to go ahead. He was told it had been decided the operation should go ahead. Joshua died on the operating table later that day.