Less than half of the staff working in the Department of Health are proud to work there, said a survey of over 2,000 employees.
The annual poll showed only 35% of DH employees would recommend their workplace as "a great place to work" and over two-thirds do not feel motivated to achieve the department's objectives.
Just over a third said they have confidence in the DH's leadership and ability to manage change.
Only 12% agreed with the statement that DH's changes are "usually made for the better" and 27% of DH employees said they "had no clear understanding" of the department's objectives.
"Staff satisfaction has remained broadly level in a year of change. Areas of improvement included how interested and challenged staff were in their jobs.," said a DH spokesperson.
"We will be taking action based on the survey findings and hope to make improvements this year."
Almost two-thirds (62%) of DH staff members surveyed said the department "does a good job" in improving the well-being of the population of England.