Documents obtained by the ABC reveal public servants are becoming "increasingly disassociated" with their superiors and feel their work is not valued, which may be reducing their productivity.
The Freedom of Information documents reveal the department has been concerned by cultural problems ever since it merged with the former customs agency in 2014 and the Australian Border Force was launched.
Each year the department asks staff to rate the leadership skills of their bosses, consider whether their colleagues are honest and reflect on their overall job satisfaction.
The results at immigration have been among the worst in the federal public service since 2014 and the department has acknowledged the problem cannot be fixed overnight.
"Staff have become increasingly disassociated from the department's culture and achievements and its leadership," an internal review of the survey said.
"These results are significantly lower than Australian public service wide results.
"Analysis of the data shows that the perceived quality of both an immediate supervisor and the senior executive staff leadership has a significant effect on staff engagement."
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