The Mexican actress set up a meeting in October between Hollywood star Sean Penn and Guzman, who was on the run at the time.
Prosecutors say she may have received money from Guzman to launch her tequila business last year.
She denies any wrongdoing.
Ms Del Castillo, who also has American citizenship, was called in for questioning shortly after Guzman's arrest.
But she failed to turn up at the Mexican consulate in Los Angeles, where she lives.
The new order is valid in Mexican territory only. If she returns to her native country, she will be detained and questioned as a witness.
Her lawyer in the US, Harland Braun, has said that Ms Del Castillo is prepared to talk to the authorities "if we receive proper information and credentials".
"She's not hiding anything. There's no problem locating her. Everyone knows she has lawyers, publicists, agents," Mr Braun told AP news agency.
On Wednesday, Ms Del Castillo sought an injunction in Mexico to prevent her arrest.
Mexican prosecutors said they respected her decision and "the principle of presumed innocence," said Attorney General Arely Gomez.
Guzman was captured by Mexican troops in the northern city of Los Mochis on 8 January.
He was taken back to the Altiplano high security jail near Mexico City, six months after escaping through a tunnel.
Guzman was the founder of the brutal Sinaloa Cartel, which smuggled vast amounts of drugs into the United States. Mexico is seeking his extradition to the US.
Ms Del Castillo and Guzman exchanged dozens of messages before she and Sean Penn met him in northern Mexico.
Some of the messages seem to mention business deals, Ms Gomez told El Universal newspaper last month.
"They mention 'the order,' 'we're in business,' 'let's go together'. There's a great deal we still need to find out," said Ms Gomez.
Last year, Kate del Castillo launched her own tequila brand, Honor del Castillo.
She would have been involved in money laundering if she had received money from Guzman for her business, explained Ms Gomez.
Kate del Castillo is best known for her portrayal of drug boss Teresa Mendoza in the soap opera La Reina del Sur (Queen of the South).
Mexican prosecutors have issued an order to locate and question actress Kate del Castillo over her links with the imprisoned drug baron, Joaquin "El Chapo" Guzman.