The attorney general's office said in a statement that a tribunal approved an arrest warrant in view of extraditing him following a request from the US state of Texas.
A US federal court in Texas wants to put Chapo on trial on charges of organized crime, drug trafficking, money laundering and homicide, the statement said.
Mexican prosecutors had obtained a similar warrant in July following a request from California, but Guzman's lawyers filed a petition against the order and a court suspended it last month.
President Enrique Pena Nieto's decision to try Guzman in Mexico instead of immediately extraditing him to the United States last year has come under scrutiny since his latest escape.
The powerful Sinaloa drug cartel kingpin also broke out of a maximum security prison in 2001 and was captured in February 2014 after a 13-year manhunt.