The prosecution says Otto Perez Leal illegally used government money to finance a re-election bid as mayor of the city of Mixco.
He lost the election and then lost his immunity from prosecution when his term ended yesterday.
He's the son of Otto Perez Molina, who resigned from the presidency in September after thousands of Guatemalans took to the streets to protest alleged corruption in his administration.
After leaving office, he was arrested and sent to jail. Prosecutors accuse him of illicit association, customs fraud and bribery.