South Sudan president says failure to pay the money was "caused by weak governance".
Using a speech to mark independence day, South Sudan's President Salva Kiir has apologised to civil servants who went without salaries for several months, Juba's Radio Miraya quotes him as saying.
Mr Kiir said the failure to pay the money was "caused by weak governance" in the departments that are supposed to raise funds and pledged to personally get involved in the issue.
Last month, the finance minister was unable to present the annual budget because MPs walked out over the salary issue, Reuters news agency reported at the time.
The eighth anniversary of independence in South Sudan is not being marked by big celebrations as there is a shortage of money, the information minister told Juba's Eye Radio on Monday.