Speculation has been rife for some time that all is not well within the Department for Children, Education, Lifelong Learning and Skills.
Now independent research, commissioned by the Assembly government, has confirmed that there are internal tensions and infighting.
The biggest complaint from staff is the loss of expertise due to constant restructuring, says the survey conducted by Beaufort Research.
Two years ago, the Welsh qualifications authority ACCAC and the post-16 learning body Elwa merged with the department as part of a plan by Rhodri Morgan, First Minister, to end the quango state.
One respondent said: "Bringing the quangos in has changed our basic relationship with officials and, to my mind, in a negative way."
Another said: "Many of the people we deal with in the department don't understand FE; some have never been inside a college."
Only one survey respondent said they had seen an improvement in the department since the merger.
Interviews with Assembly government staff also revealed concerns about poor communication within the department.
According to the survey, years of restructuring have resulted in divisions between children and education services, despite the merger.
Rex Phillips, Wales organiser for the teachers' union NASUWT, said there had been problems about knowing whom to contact, but that this situation was improving.
"Now our major criticism is the lack of joined-up thinking when it comes to areas such as 14-19 learning pathways; the different departments aren't talking to one another."
Elaine Edwards, general secretary of Welsh-medium union UCAC, agreed that there was a lack of communication within the department.
But some unions praised changes in management since the survey was conducted last autumn.
Dr Philip Dixon, director of ATL Cymru, said the arrival of David Hawker, the department's new director, had made a positive impact.
"I think he has given the department stability and people are more confident; they know what they should be doing," he said.
The government said that a "significant" number of department staff did have experience in education and that it would use the findings to improve operations: "Internal processes are being put in place to ensure we join up more effectively, both internally and externally."