The man detained, Sergio Antonio Mora Cortez alias 'Toto', was arrested along with five other members of the Zetas.
Mora Cortez was directly in charge of Julian Zapata Espinoza, alias 'El Piolin' (Tweety), who is under arrest for the killing of the US Immigration and Customs Enforcement (ICE) agent, the Mexican navy said in a statement.
Mora was detained in Saltillo, Coahuila state, near San Luis Potosi state, where the US agent, Jaime Zapata, was slain February 15 and his colleague Victor Avila was wounded, it added. The US agents were attacked while driving from the northern city of San Luis Potosi to Mexico City in a region plagued by drug violence.
The killing of US agent Zapata was the first since Enrique "Kiki" Camarena was kidnapped, tortured and killed while working undercover for the US Drug Enforcement Administration 26 years ago. More than 34,600 people have been killed in rising drug related violence in Mexico since December 2006, when President Felipe Calderon deployed soldiers and federal police to take on organized crime.