The EZLN and many Chiapas residents accused the ruling Institutional Revolutionary Party (PRI) of complicity, and following the change of government in 2000, survivors alleged that the investigation was being stalled, with authorities refusing to question or arrest suspects in the attacks.

Las Abejas, composed of people from 48 indigenous communities in the highlands of Chiapas, engaged in activism, issuing communiqués that denounced violence through actions centered around fasting and prayer.

In November 2006, 100 men and 100 women members of the Abejas organized a peace and justice caravan to Oaxaca, to show their support for the Popular Assembly of the Oaxacan People (APPO) and denounce the repression and violence perpetrated by the state and federal governments.

On August 27, 2007, Martín Rangel Cervantes, writing in national daily El Universal, stated that a federal judge assigned to the Acteal case sentenced, on July 22, 18 persons for their responsibility in this massacre.

In 2014 the US Supreme Court turned down a case filed by the survivors of Acteal massacre against Connecticut resident and former Mexican President Ernesto Zedillo on grounds of "sovereign Immunity" as a former head of state.