The high court said it would set aside half an hour of hearings for each of the 321 challenges, most of which came from the states of Puebla, Oaxaca, Michoacan, Guerrero, Chiapas, Morelos and Jalisco.
The Supreme Court said it would conclude all the hearings by June 18th and then deliberate before handing down a sentence, El Universal daily reported.
The law was expected to give Mexico's indigenous populations - many of whom are marginalized by poverty - a greater degree of political autonomy and guarantees for better living conditions.
But the final law passed by Congress was a watered-down version of the original agreement between the federal government and indigenous representatives of the Zapatista National Liberation Army (EZLN) in the southern state of Chiapas. The law struck key provisions dealing with indigenous rights over land and natural resources.
While the Supreme Court debates the law, congressional representative on indigenous issues Senator Rutilio Ruiz Escandon Cardenas announced he would travel with members of the Senate Peace and Reconciliation Commission to Chiapas.
Escandon Cardenas, of the left-of-center Party of Democratic Revolution (PRD), said it was necessary to return to the negotiating table with indigenous representatives. The EZLN broke off all contact with the government following the Senate's passing of the controversial law.
The PRD legislator said the most urgent task is to have a meeting of the two sides to express their differences and start proposing solutions to indigenous demands.