A manhunt began late on Saturday night after the disappearance of Guzman – head of the powerful Sinaloa cartel.
Authorities found a tunnel in Guzman’s cell. The 1.5km escape route led to a building under construction outside the prison.
Mexico’s National Security Commissioner Monte Alejandro Rubido said 18 people were being taken to Mexico City for questioning over Guzman’s escape.
The narcotics kingpin was last seen in the showers of the Altiplano prison, Mr Rubido said. Flights have been suspended at the nearby Toluca airport.
Guzman was arrested in February 2014 and faces multiple drugs trafficking indictments both in Mexico and the US.
His Sinaloa cartel, named after the area of Mexico in which it was founded, is an international drugs trafficking organisation believed to control most of the major crossing points for drugs at the US/Mexico border.
He was first arrested in 1993 and sentenced to more than 20 years in prison on drug trafficking charges. He escaped in 2001 by bribing guards to help smuggle him to freedom.