Guatemala`s top prosecutor`s office tweeted late on Wednesday that Attorney General Thelma Aldana had sought an arrest order for Perez. It said the charges were illicit association, taking bribes and customs fraud.
An official from Aldana´s office confirmed that high-impact judge "B" had issued an order for Perez`s detention.
Perez´s lawyer said the president, who had been deemed a flight risk, would present himself at court at 8 a.m. on Thursday (1400 GMT).
Perez, who cannot run for re-election under the constitution and is supposed to remain in office until a handover in January, has denied any wrongdoing and has repeatedly said he would not resign over the scandal.
Perez`s conservative administration has spent much of this year mired in public protests and scandals over corruption allegations against senior officials, several of whom he fired during a cabinet purge in May.
Prosecutors have said it is highly probable that Perez was involved in a customs racket dubbed "La Linea," or the line, due to a phone hotline used in the scandal, in which importers avoided paying customs duties in exchange for bribes.
Vice President Roxana Baldetti resigned last May after she was linked to "La Linea." She denied any wrongdoing but has been arrested and charged with illicit association, bribery and fraud over the customs racket.
A judge appointed to oversee the case could decide that Perez should await trial behind bars.
If Perez is jailed, the judge would be able to order the end of his presidency, prosecutors have said. According to the constitution, current vice president Alejandro Maldonado would step in.
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