"The president has submitted his resignation" to parliament, the newspaper quoted Jorge Ortega as saying in its online edition, Reuters reported.
On Wednesday a Guatemalan judge issued a detention order for Perez amid a graft scandal that has gutted his government and plunged Guatemala into chaos days before a presidential election.
Perez had his immunity from prosecution stripped by lawmakers on Tuesday in a fast-moving climax to a crisis that has roiled Guatemala for months. The 64-year-old retired general was elected on a ticket to combat crime and corruption.