An inquiry by Chief Medical Officer Professor Liam Donaldson found that more than two dozen other NHS institutions have each stockpiled more than 500 organs, body parts or corpses of stillborn babies and fetuses.
Oxford Radcliffe Hospitals is listed as having 4,400 organs or parts, while Great Ormond Street children's hospital in London has 3,800.
Hospitals keep parts for research and teaching but there is an issue over whether parents have an opportunity to give their consent.
The institutions listed as retaining organs said they were used to help them carry out "valuable" research.
Some 25 hospitals accounted for 88% of the retained organs, at least 16,500 of which were retained in contravention of the law, said Health Secretary Alan
The chief executive of the United Bristol Healthcare Trust (UBHT), which runs the Bristol Royal Infirmary where the organ retention scandal first emerged during an inquiry into infant mortality rates, led the apologies.
Apology for distress
But Hugh Ross said the fully informed consent of parents and families for the retention of their child's and relative's organs and human material in hospital post mortems had been sought and gained for several years.
Mr Ross said: "This trust fully accepts that in the past the information given to parents and relatives about the reasons for retaining organs was not as full and frank as today's standards demand.
"We echo the chief medical officer's apology for the distress this very difficult issue has caused many people." Mr Ross said the trust had inquiries from 300 parents and relatives during the soon-to-be-published report on the Bristol Royal Infirmary Inquiry about the organs it has retained.
Chief executive of the Oxford Radcliffe Hospitals Trust David Highton said: "This Trust carries out post mortems on behalf of the coroner.
"In some cases organs will have been removed and retained for further study, teaching and research.
Although in past years normal procedure did not involve providing information to relatives, I accept that this is no longer appropriate.
We now follow this guidance, which ensures relatives are given full information before being asked about organ retention, and that their wishes are
He continued: "I and my colleagues at the Oxford Radcliffe Hospitals Trust are deeply sorry for any distress this may have caused."
Southampton General Hospital, one of the UK's major teaching and research centres, retained 1,300 brains and 220 hearts for research into diseases such as CJD and Alzheimers.
Spokeswoman Marilyn Kay said "one or two" dated back to the 1970s with the majority coming from the 80s up to the mid 90s.
She explained that all the organs were catalogued and the hospital had never taken all the organs from one body.
"We accept that many organs were retained at a time when much less explicit consent was sought from relatives," she said.
Mrs. Kay added that the hospital had worked hard with families to set up new guidelines for consent independent of the government. These have been in force since 1999.
"We also hope that people recognise that medical research does have a valuable role. It enables doctors to save lives," Mrs Kay said.
Institutions holding more than 500 body parts, organs and corpses from stillborn children and fetuses
Royal Liverpool Children's (Alder Hey): 6,900
Oxford Radcliffe Hospitals: 4,400
Great Ormond Street Hospital for Children: 3,800
Royal Brompton and Harefield: 3,500
Queen's Medical Centre Nottingham University Hospital: 2,700
Newcastle upon Tyne Hospitals: 2,700
North Bristol: 1,700
Southampton University Hospitals: 1,500
Leeds Teaching Hospitals: 1,500
United Bristol Healthcare: 1,400
Birmingham Children's Hospital: 1,100
Havering Hospitals: 1,000
Central Sheffield University Hospitals: 900
Guy's and St Thomas' Hospital: 900
Addenbrooke's Hospital: 700
Basildon and Thurrock General Hospitals: 700
Walton Centre for Neurology and Neurosurgery: 500
Imperial College London: 4,200
Institute of Neurology: 1,400
Institute of Child Health: 900
Institute of Psychiatry: 600
King's College London: 500