Intelligence agencies of the government say Gildardo Lopez Astudillo, known as "El Gil" is a leader of the Guerreros Unidos drug cartel.
It alleges he gave the orders to abduct and kill the students.
There have so far been 111 arrests over the disappearances.
The Mexican attorney-general's office says its investigations show the Guerreros Unidos gang were handed the students by corrupt police in Iguala.
The office has said because Guerreros Unidos thought the students were members of a rival gang, they murdered them and then disposed of the bodies by burning them at a rubbish dump outside the city.
Official accounts contrast with a report issued by an international group of experts appointed by the Inter-American Human Rights Commission (IAHRC).
Their report earlier this month alleges that the Mexican authority's investigations were deeply flawed, and included the disappearance of key evidence.
