Healthcare Commission chair Sir Ian Kennedy has written to health secretary Alan Johnson to protest after the Department of Health rejected proposals aimed at reducing deadly blood clots.
The commission had called for trusts to be assessed against a new indicator relating to the prevention of venous thromboembolism.
It wanted the new measure to be included in annual reviews to be carried out by new regulator, the Care Quality Commission.
The idea was strongly supported by "key external stakeholders", according to a report discussed at last week's commissioners' meeting. But the report states: "The DH has unfortunately rejected this proposal as not being a national priority."
At the meeting, Sir Ian said: "I find this at best disquieting. We have made safety our highest priority." He added: "I don't see how we can... not make a point about something which is a very significant hazard to a large number of people in hospital."
Commissioner David Haslam, who is also the president of the Royal College of GPs, said the condition was responsible for far "more deaths than healthcare associated infections multiplied".
He said he approved of Sir Ian writing to Mr Johnson expressing the commission's concerns.
DH guidance issued last year provided trusts with a checklist to help identify susceptible patients. It followed HSJ findings revealing that more than half of trusts were ignoring calls by the chief medical officer to carry out checks aimed at prevention.
A 2005 health select committee report said 25,000 people died from venous thromboembolism contracted in hospitals each year.
Commission chief executive Anna Walker said she understood the DH did not want another scored indicator on venous thromboembolism but further work was being discussed.