During the presidency of Carlos Salinas de Gortari (1988-1994) he founded the Center for Investigation and National Security (CISEN) and headed the Commission for Attention to Crimes against Health of the Attorney General's Office (PGR).
During Miguel de la Madrid he led the dismantling of the repressive arm of the government, the Federal Security Directorate (DFS) and allowed a new perspective of Human Rights.
This incident caused, in addition to a diplomatic conflict with Guatemala, the displacement of 40,000 Mayan indigenous people who were given legal and physical security in territory belonging to the states of Campeche and Quintana Roo.
During his assignment there was a comprehensive, multidisciplinary and open approach to international cooperation within which the relationship with the United States, Colombia, Central America and other Latin American countries was redefined.
He was decorated by the governments of France, Germany, Yugoslavia, Jordan, Egypt, Italy, Spain, Austria, Romania, Venezuela, Senegal, Argentina, Japan and Great Britain.
For his part, Carrillo Olea has always proclaimed his innocence and nothing has ever been proven; He insisted that the complaints were invented by Graco Ramírez, the Bishop of Cuernavaca, Luis Reynoso Cervantes, and President Ernesto Zedillo.
[4][5] In 2011, Carrillo Olea wrote México en Riesgo, Una visión personal sobre un Estado a la defensiva (Mexico at Risk, A Personal View of a State on the Defense), which is a reflection on the Mexican security apparatus during the presidencies of Luis Echeverría, José López Portillo, Miguel de la Madrid and Carlos Salinas de Gortari; as well events such as the Tlatelolco massacre of October 2, 1968, the 1973 Chilean coup d'état, the 1985 Mexico City earthquake, the collapse of the computer system during the 1988 Mexican election, and his own governorship of Morelos.