Membership to the system and the level assigned (candidate, I, II, III, emeritus) dependents on scientific productivity and is evaluated by peer committees.

Members of SNI, both Mexican and foreign, receive a monthly stipend directly from CONAHCYT only if they work in institutions or universities located in Mexico.

Mexican nationals working full time on research-related activities but ascribed to institutions located outside Mexico are eligible for membership but not for the stipend.

CONAHCYT also manages 26 public research centers (CPI[3]) located in several parts of Mexico and dedicated usually to a narrow field of science.

This was criticized, because it was seen as the director overstepping his authority and even violating the Constitution as it denied the autonomous nature granted to Mexican CPIs.