The order is not for arrest, but for Perez Molina to declare before Judge Miguel Angel Galvea, who granted the request yesterday from Attorney General Thelma Aldana, she told Canal Antigua television.
The president will have to appear on accusations of illicit association, fraud and receiving bribe money in a customs fraud scandal in which the vice president has already been jailed and some of his Cabinet ministers have stepped down.
Aldana said there is a preliminary investigation underway about the president's possible involvement in the fraud ring.
Perez Molina, 64, has maintained his innocence and vows to face the legal process. No formal charges have been filed. His attorney, Cesar Calderon, told The Associated Press that the president will appear voluntarily as soon as they have confirmed the order was issued.
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It is the first time a sitting Guatemalan president has faced legal prosecution, though several have faced corruption charges after leaving office.
The corruption scandal, uncovered by prosecutors and a UN commission probing criminal networks in Guatemala, involved a scheme known as "La Linea," or "The Line," in which businesspeople paid bribes to avoid import duties through the customs agency.
The ring is believed to have defrauded the state of millions of dollars.
The scandal has already claimed the job of former Vice President Roxana Baldetti, whose ex-personal secretary was named as the alleged ringleader.
Baldetti resigned May 8 and is currently in jail awaiting trial on accusations she took millions of dollars in bribes.