Government spent over N$275 million paying out accumulated leave days for 2 500 civil servants who left during the 2016/17 financial year.
A human resources audit report compiled by the Public Service Commission (PSC) for the period attributed the massive payout to the poor record keeping by ministries and government agencies.
The report states that some ministries were not complying with rules that guide the granting of leave which allows public servants "at least 24 consecutive days and 18 days for vacation leave" with full remuneration in a year.
"It seems that this provision is not being adhered to, and as a result leading to staff members piling up leave days," it added.
The education ministry paid out the biggest amount of N$180 million to 1 100 people, while the health ministry with N$66 million to 815 people.
In third place was the agriculture ministry which paid N$4,2 million to 126 employees, with the international relations ministry forking out N$2,2 million.
The urban development ministry paid out N$1,7 million to 13 people, while the youth ministry paid out N$1,5 million to 15 people.
According to the report, the international relations ministry did not provide the number of people who were paid out.
Other ministries, namely fisheries, trade and industrialisation and justice, and the attorney general's office, provided some numbers of those who were paid for accrued leave, but did not disclose the amounts.
The report quotes PSC chairperson Markus Kampungu as saying the commission had noticed a worrying trend with regard to the government's human resources management systems.
He said there were "anomalies in the recruitment process, filing, and the administration of pension funds, as well as the medical aid schemes".
"Leave administration calls for special attention, proper management and supervision. To address the human resources management shortcomings and anomalies, managers and supervisors need to be held accountable if we are to take service delivery to the next level," Kampungu stated.
Auditor general Junius Kandjeke has in the past raised the issue of mismanagement of staff leave at ministries and government agencies.
He also pointed out that some employees on government's payroll have been claiming "false leave".
Kandjeke thus advised government to improve its systems to prevent unnecessary spending on civil servants' benefits.
The spokesperson at the Office of the Prime Minister, Saima Shaanika, did not respond to questions sent by email.