The proportion of DoH civil servants who thought their department was well run was 35 per cent lower than the average across the civil service.
The biennial survey questioned 169 of the DoH's most senior civil servants on how they rated its performance as well as their own.
Other disappointing results were that only 14 per cent of the DoH's civil servants felt its top team displayed a 'culture of effective teamwork', and that only 37 per cent said they had confidence with the civil service leaders within the DoH.
The first survey was carried out in 2004 and the latest figures reveal a drop in morale in some areas. In 2004, 47 per cent of senior DoH civil servants said they had confidence in civil service leaders within their department.
The survey does show that staff at the DoH are committed to their jobs.
Ninety-eight per cent of the civil servants questioned said they were committed to seeing the DoH succeed, and 91 per cent were 'willing to put in a great deal of effort beyond what is normally expected to help my department succeed'.
Wendy Jones, DoH national officer for the First Division Association, which represents senior civil servants, said: 'The survey results are alarming.
'There have been constant, dramatic changes at the DoH over the past few years and the staff are obviously fed up with permanent revolution.
'Clearly this has impacted on leadership, morale, team working and workloads. The FDA will be engaging with the department as soon as possible to address these serious issues.'
The DoH said: 'Last year was a difficult year, with much internal and external change, but our new leadership team of NHS chief executive David Nicholson and permanent secretary Hugh Taylor, appointed in September and December respectively, is now in place and providing clear direction.
'We are clear that our outlook for 2007 is positive and the department is learning from its mistakes.'
It added: 'Fundamental improvements to the management and governance of the department have been put in place to make us stronger and more efficient in the long term.'
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