Presidential spokesman Jorge Ortega said in a statement early Thursday that the president has stepped down.
Under Guatemalan law, Vice President Alejandro Maldonado Aguirre will take office to serve out Mr. Perez Molina`s term, which ends in January.
The whereabouts of Mr. Pérez Molina, a 64-year-old former general, were unknown early Thursday, although his lawyer had said in recent days that, if charged, the president would turn himself in to avoid being captured by police.