An independent expert review which considered the treatment of 2,500 patients operated on during 1993-95 condemned the record of James Wisheart as "significantly poorer" than that of his colleagues.
Mr Wisheart retired early as medical director of the hospital in December, when he also stopped doing clinical work.
On Monday, the 59-year-old surgeon announced his retirement from the National Health Service. He and a fellow surgeon, Janardan Dhasmana, already face a separate General Medical Council investigation following an inquiry into the paediatric cardiac surgery at the hospital.
Last year, it was revealed that nine out of 13 babies died when undergoing "switch" operations and other surgical techniques to repair heart defects at the hospital between 1990 and 1995. The failure rate was around two out of three, compared with a national average of one in 10.
A GMC spokesman said yesterday: "Our investigations into complaints about paediatric cardiac surgery at the Bristol Royal Infirmary are well advanced."
Mr Dorrell revealed, in answer to a question from Robert Key, the Conservative MP for Salisbury, that the Department of Health inquiry would not start until the GMC investigation was over.
"I am mainly concerned about the response made at that time by the trust's management to these matters," he said.
"In the past two years, the trust has taken steps to improve the services, appointing a new paediatric cardiac surgeon and transferring services to new specialist facilities at the Bristol Children's Hospital.
"However, questions remain about the handling of these difficult issues. which may have wider implications for the NHS as a whole."
He added: "It is vital the facts are ascertained; that any failures are identified and that lessons are learnt in Bristol and throughout the country to prevent similar situations in future."
The original inquiry into the deaths was carried out by Marc de Leval, consultant paediatric surgeon at Great Ormond Street Children's Hospital in London.
It reported in January, 1996, and and led to the appointment of a new consultant. Ash Pawade now carries out all the paediatric cardiac surgery at the Bristol Children's Hospital.Reuse content