Employees in 196 schools were asked to rate their schools on 51 criteria.
Pupil behaviour was singled out as a problem, but workload scored almost highest in terms of dissatisfaction. Next was staff self-esteem, followed jointly by morale and a fair pay structure.
Communication between the senior managers and staff was also rated low.
But, staff do rate their schools highly on relationships between colleagues. Most said they had a good relationship with their head of department. The vision of headteachers was also highly regarded.
John Bangs, head of education at the NUT, said the survey by consultants Kirkland Rowell showed the concerns of teachers had remained relatively unchanged over the years, despite the policies such as the workload agreement.
Anita Kapila, a science teacher from Burnham upper school in Buckinghamshire, said: "Poor behaviour can lead to low morale. It can get lonely in class. But there's a strong spirit in the department, where I'm well supported."
Sue Wade, a teaching assistant at Hethersett high school near Norwich, said: "The pay structure is dreadfully unfair for us. I could go down the road and get more."
John Dunford, general secretary of the Association for School and College Leaders, said the findings showed how pressure on heads was "inevitably"
passed to other staff.