Jose Manuel Garcia Soto alias "El Safado" or "The Crazy One" was arrested on Saturday in the northern state of San Luis Potosi, the Secretariat of Public Security said in a statement.
He is thought to be linked to the death of ICE agent Jaime Zapata, 32, who was shot and killed on February 15 while driving in the same state, wracked by drug violence. A second ICE agent was wounded in the ambush.
Zapata and his partner were not armed when Mexican gunmen attacked them.
Garcia, 30, told police he had operated under the command of Julian Zapata Espinosa, alias "El Piolin" (Tweety), in a Zetas cartel cell.
Federal police said Garcia Soto oversaw drug trafficking, extortion, kidnapping and robbery operations and was involved in the killing of members of rival gangs. No formal charges have been filed against him or the other suspects.
Zapata was killed after gunmen forced stopped his SUV on a highway in San Luis Potosi. One of the suspects who allegedly took part in the shooting said gunmen mistook the agents' SUV for a vehicle used by a rival gang.
San Luis Potosi borders two northern states where the Zetas and the Gulf cartel have waged bloody turf wars. Zapata and Avila were temporarily detailed to the ICE attache office in Mexico City and were driving from the northern city of Monterrey to the capital when they were attacked.
Mexican authorities have captured two other members of the cartel linked to the attack on the ICE agents.
The weapon used to kill Zapata came from the United States, according to US officials.
Last month the US offered a $5 million reward for help in finding Zapata's killer, with the bounty offered in addition to a 10 million peso (US$839,000) prize from the Mexican government for information leading to the murderer's arrest.
A financier in the Zetas drug cartel was arrested in March in connection with the murder, along with 16 other gang members, but at that stage the person suspected of actually firing the 7.62mm caliber pistol that killed Zapata was still believed to be at large.
Los Zetas is one of seven major drug gangs operating in Mexico whose bloody clashes have left over 34,600 people dead since December 2006, when the government launched a military crackdown that has so far failed to stem the scourge of violence.
Sources: AFP, NPR