Senior public servants have been told to improve their management skills and build better relationships with staff.
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The warning came after an annual survey, commissioned by the Australian Public Service Commission, found junior staff were more likely to be unhappy with their bosses.
The same survey also found 41 per cent of public servants considered communication with SES ranks within their agency to be effective.
"Employee satisfaction with immediate supervisors varies noticeably by respondent classification level," an APSC statement said.
"This represents a challenge for supervisors in the SES and EL levels, to strive for more positive employee perceptions of their leadership behaviours by their APS level employees."
Almost 90 per cent of SES officers described their supervisors as having integrity, being driven and capable of achieving results. For the rank-and-file it was closer to 75 per cent.
"Across all 10 leadership competencies, APS level employees reported lower levels of satisfaction with their immediate supervisor than did EL and SES employees," the statement said.
"The challenge for supervisors of APS staff is to be mindful of the need to connect better with their employees.
"Immediate supervisors can influence these connections by improving their communication with their employees."
Those who work in specialist, policy and regulatory agencies tend to be happiest with the performance of their immediate boss. Those in public-facing operational roles have lower satisfaction levels.
The survey also found public servants in small agencies were happier with the boss while those in larger offices were harder to please.
"In some cases, employees may not work in the same location as their immediate supervisor," the commission said.
"This may lead to additional staff management challenges that impact the relationship between an employee and their immediate supervisor."
Despite this, the commission said satisfaction with bosses was high and "a key strength of the APS".
"Census respondents rated their immediate supervisors most positively on achieving results and demonstrating personal drive and integrity," the spokesman said.
"Supervisors were rated marginally less positively on shaping strategic thinking and communicating with influence."
