The authorities say the Zetas killed around 150 people inside the Piedras Negras prison, just over the US border, before incinerating the bodies or dissolving them in acid.
Humberto Moreira is due to appear in a Madrid court on Friday following his arrest in an investigation into money laundering that reportedly also includes evidence that he was working for the Zetas cartel.
Humberto Moreira, who was once a close ally of President Enrique Peña Nieto, is wanted by US authorities investigating allegations of money laundering and other crimes.
According to official figures there are 24,238 people currently disappeared in Mexico. With the authorities doing little to find them, some relatives of the missing have formed groups to search for their loved ones themselves.
The twister struck Ciudad Acuña across from Texas early on Monday, lifting large vehicles and buses onto buildings. Most of the dead were outdoors at the time, officials said.
The Zetas cartel turned Mexican ranches into extermination camps, kidnapping at least 300 people and burning them in makeshift "kitchens."