The national health department says provinces have paid up but the head of lab services denies this.
The second industrial action in as many years is likely to stretch into its second week.
The nationwide industrial action is expected to last at least until Friday and could affect patients living with conditions such as cancer and HIV.
Unions say they will not accept anything less than 7.3% wage increases.
The Gauteng health department says the National Health Laboratory Service will not suspend its services to it despite money being owed.