Smaller government departments are churning through staff at a rate triple that of the public sector average.
The Serious Fraud Office and Ministry of Women's Affairs had the highest staff turnover rate of 30 per cent in the past financial year.
That amounted to almost a third of staff leaving in a 12-month period.
Ministry of Pacific Island Affairs came in third with a turnover rate of 24 per cent – almost a quarter of all employees.
The public sector unplanned turnover average is 11 per cent.
But agency heads have blamed significant changes in their departments for the struggle to retain staff.
The high staff turnover follows report cards that highlighted other inefficiencies in Women's Affairs and Pacific Island Affairs.
A State Services Commission report identified poor policy, limited skills, high overheads and a heavy reliance on bigger agencies at those ministries.
Women's Affairs chief executive Rowena Phair defended the high turnover rate. "The ministry has been through a significant change process over the past 18 months that has resulted in improved performance and efficiencies and, inevitably, higher staff turnover."
Serious Fraud Office general manager corporate services Victoria Currey also said an organisational review contributed to staff turnover.
"As a small office within the public sector, any personnel changes can have a greater impact compared to other organisations."
At Pacific Island Affairs, chief executive Colin Tukuitonga said the agency was rebuilding. "When organisations change, a high turnover is inevitable."
The three agencies with the highest turnover were also the smallest departments, with 35 to 40 staff each.
The commission report on staff turnover said fewer opportunities for employees at smaller agencies forced staff to look elsewhere.
Turnover rates were also more volatile in smaller agencies, where just a few people leaving an organisation of 30 could skew results.
An average pay packet of $65,179 failed to retain the departing staff in the small agencies. The fraud office and Women's Affairs both refused to respond to a question on the average salary of staff, while Pacific Island Affairs said its average was $83,700.
Across all state agencies, policy analysts and IT staff were most likely to quit their jobs, while managers and inspectors had the lowest turnover rates. The turnover rate of IT staff doubled over the past year, from 8 to 16 per cent.
Call centre workers on the other hand appeared happier in their jobs, with the turnover rate having dropped from 28 to 13 per cent over the past three years.
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