Presidential spokesman Jorge Ortega has confirmed in a statement on September 3 that the president has stepped down.
On September 1, Guatemala’s congress voted to remove Otto Perez Molina’s immunity from prosecution amid corruption allegations.
Prosecutors accuse the president of masterminding a scheme to defraud the customs service of millions of dollars, allegations he denies.
The judge has barred Otto Perez Molina from leaving the country.
The president, whose term runs out in January, will now be summoned to appear before a court.
The detention order was signed by Judge Miguel Angel Galvez, the prosecutor’s office said.
On September 1, all members of congress present at the vote endorsed a move to strip Otto Perez Molina of his immunity.
They included members of the president’s own party.
A previous vote to remove Otto Perez Molina’s immunity failed last month.
Since then, more details of the corruption scandal have emerged and calls for the president to resign have increased.
Investigators allege that government officials received a cut from bribes paid by businesses seeking to evade import duties.
Guatemala’s VP Roxana Baldetti and a string of top officials have been forced to resign over the scandal.
Roxana Baldetti is in jail awaiting trial on charges of taking millions of dollars in bribes.
Otto Perez Molina was stripped of his immunity just days before presidential elections on September 6.
Some protesters have demanded that the polls be postponed, but officials argue that it would be against the law.
Otto Perez Molina is barred by the constitution from standing again.
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