The research, part of the annual Civil Service People Survey, showed 33 per cent of respondents agreed or strongly agreed with the statement: "I feel that the commission as a whole is managed well." This figure was eight percentage points lower than the average result across the civil service.
Thirty-eight per cent of the 369 of the commission's 422 staff polled either disagreed or strongly disagreed with the statement and 29 per cent said they neither agreed nor disagreed.
The survey also found 24 per cent believed the commission's board had a clear vision for its future – 11 percentage points lower than the civil service average.
Just 18 per cent said they felt change was managed well at the commission, 10 percentage points lower than the average.
However, 49 per cent said they felt a "strong personal attachment to the commission" and 72 per cent said they had confidence in the decisions made by their manager. Both of these figures were three percentage points higher than the civil service average.
The survey revealed 31 per cent of staff polled thought it was "safe to challenge the way things are done in the commission".
Fourteen per cent of respondents said they had experienced bullying or harassment at work in the past 12 months. Ten per cent said they had experienced discrimination in the same period.
A spokeswoman for the commission said: "The commission will be conducting a full analysis of these results, however, at first glance, it's clear there are areas in which the commission can improve employee engagement, including leadership and managing change.
"We will also look closely at the results on discrimination, bullying and harassment, as we are concerned about the responses in these areas, but it is encouraging that there are areas in which staff members clearly think the commission is doing increasingly well, notably team-working and line management."