The move by the Government's race watchdog comes after a stream of complaints by CPS staff that they have been racially harassed and victimised.
This summer alone, two separate employment tribunals found that CPS prosecutor Maria Bamieh had been racially discriminated against by her employer.
CRE officials says its investigators will go into the CPS's offices next month under the powers it holds under the Race Relations Act.
The move comes after months of negotiation between the two bodies in which they attempted to hammer out a plan to improve matters at the CPS.
But the CRE says it was not satisfied with the CPS's assurances and has decided to use this ultimate power for only the fourth time in five years.