Finance directors averaged £109,872 in 2008/9 (up 7.1% on 2007/8), HR directors £88,795 (up 7.4%) and nursing directors £92,617 (up 8.4%).
The figures contrast sharply with GP practices where global sums have been frozen for three years and more than half of partners had been forced to take a pay cut.
The figures exclude PCTs although details of these will be published next month.
A total of 66 trusts took part in the survey. There was a strong relationship between the size of a trust and salaries paid to its most senior managers.
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