A judge has issued an arrest warrant for Guatemalan President Otto Perez, who faces prosecution for allegedly masterminding a huge fraud scheme, according to the country's prosecutor-general.

The development comes a day after he was stripped of his immunity due to organised corruption charges against him.

RELATED: Can corruption be wiped out in Guatemala?

Prosecutor-general Thelma Aldana said Judge Miquel Angel Galvez issued the order on Wednesday afternoon on crimes of illicit association, fraud and receiving bribe money related to a widespread customs fraud ring in which the vice president has already been jailed and faces charges.

Under Guatemalan law, Perez will be automatically removed from office if remanded in custody by a criminal court.

Guatemala's attorney general also said on Wednesday that she was confident embattled Perez would be convicted of corruption, as the country's top court rejected Perez's challenge to prosecutors' moves to try him.

"This has been happening at an incredibly fast rate. If the judge decides to send him to prison after he is picked up, this might be the end of his political career," Al Jazeera's David Mercer, reporting from the Guatemalan capital of Antigua, said.

"Despite the mass protests against him, he many times said that he had no connection to this multi-million-dollar fraud."

The conservative leader is against the ropes after the Guatemalan Congress voted unanimously on Tuesday to strip him of his immunity, clearing the way for prosecutors to go ahead with their case against him.

Investigators accuse Perez of running a scheme in which businesses paid bribes to dodge taxes on their imports, defrauding the country of millions of dollars.

The scandal, which has already felled his former vice president and a string of top officials, comes as Guatemala prepares for elections on Sunday to choose his successor.

Perez, in power since 2012, is constitutionally barred from running for re-election. His term ends on January 14.

The president has been left increasingly isolated by the scandal.

Six of his 14 ministers have resigned in recent days, along with several other top officials.

Source: Agencies