Guatemalan prosecutors and a UN investigative commission accused President Otto Perez on Friday of being one of the ringleaders of a customs bribery scandal shaking the country.

Hours after Perez's former vice president Roxana Baldetti was arrested on corruption charges, prosecutors and members of the UN commission told a press conference that they had found the president was directly involved in a scheme to reduce importers' customs duties in exchange for bribes.

The allegation comes just over two weeks before general elections that will decide Guatemala's next president.

Perez, whose term ends in January, cannot run in the September 6 elections.

The UN commission's Ivan Velasquez said the investigation had uncovered evidence of Baldetti and Perez's "very regrettable participation (in the corruption scheme) at every level of the organization."

The work of the UN commission has upended Guatemalan politics.

The panel was set up to fight high-level graft and launched its investigation in May last year.

The probe has also netted the head of Guatemala's tax administration, his predecessor and several dozen other agency officials.

Baldetti resigned as vice president on May 8 after one of her top aides, Juan Carlos Monzon, was accused of running the bribery scheme.

Monzon is still at large.

The investigation is based on thousands of wire-tapped phone calls that uncovered a scheme dubbed "La Linea" (the line), named for the hotline used by businesses to contact the corrupt network of customs officers.

The scandal has sparked mass protests calling for Perez to resign.

Velasquez said the taped phone calls included references to "Number One" and "Number Two," which investigators had determined to be Perez and Baldetti.

"We have evidence that goes beyond the phone calls," he said.