Simulations for worth determination of Control and Protection System Absorber Rods (CPSARs) are carried out for a VVER-1000 reactor model employing indigenous reactor physics code system, EXCELTRIHEX-FA. Starting with the calculations of critical H3BO3 concentrations for various configurations of control groups in a fresh clean core at hot zero power (HZP), simulations of stepwise insertion of individual control group are carried out, one group at a time, to estimate the differential and integral worth. Furthermore, for some specific configurations of control groups at HZP, the integral worth of individual CPSAR of both control and protection system are calculated. Comparisons of EXCEL-TRIHEX-FA simulation results with the design calculations show reasonable agreement and also better when compared to the other international state-of-the-art code systems. Despite the deficiency of the diffusion theory for strong absorbers and cross-section homogenization approximation, the prediction capability of EXCEL-TRIHEX-FA code system is well demonstrated for CPSAR worth estimations.