The NPA made an undertaking last month to pay staff bonuses and salary increases in a staggered manner as it faced budgetary constraints.
But, more than a month later only junior staff have received the performance bonuses, while salary increases were paid to everyone.
Senior staff said they had been left in limbo as the NPA had not made it clear when they would receive the performance bonuses.
This week the NPA’s Bulelwa Makeke said payment would be made gradually in the lead-up to the end of the financial year.
The NPA now has two months to fulfill its undertaking as the 2016/17 financial year ends in March.
According to a state advocate who did not want to be named, bonuses were normally paid out between September and November each year.
The Public Servants Association laid a dispute with the NPA last year after it said it would not pay performance bonuses to all staff, citing budgetary constraints.
Rashied Daniels, of the Public Servants Association, said the NPA’s failure to pay the bonuses was “ disappointing”, but staff remained committed to their jobs.