Otto Perez Molina, 64, rejected allegations that he was the mastermind of a customs corruption scheme dubbed La Linea, or The Line.
At least 100 people are being investigated over the scheme.
A judge in Guatemala City ordered his detention on September 3 while hearings over the corruption allegations took place.
After a second day of hearings, Otto Perez Molina was again taken from court to a military prison in the capital.
Otto Perez Molina addressed the court on September 4.
“The first thing I want to deny: I don’t belong to La Linea,” he said.
The former president denied taking any bribes and promised to co-operate with the investigation.
“Your honor, I am not going to risk my dignity, my work, nor all the effort I have made for Guatemala in return for $800,000,” he said, in reference to the amount prosecutors say he received illegally.
Investigators say the scheme involved businesses paying bribes to government officials and customs officers in return for being allowed to evade import duties.
Otto Perez Molina reminded the court that he had rejected much higher bribe offers from the fugitive Mexican drug lord, Joaquin “Shorty” Guzman in 1993.
The former president led the operation that led to his arrest in Guatemala.
“After his capture, I was offered 10, 15 times more than that amount in bribes [to let him go]. I didn’t do it because that goes against my principles,” Otto Perez Molina said.
Shorty Guzman, who is the leader of the Sinaloa Cartel, was extradited to Mexico, but escaped from a high security jail for a second time earlier this year.
Guatemala’s Congress stripped Otto Perez Molina of his immunity from prosecution on September 1.
That opened the way for criminal charges to be brought against him.
Vice-President Alejandro Maldonado was sworn in as interim head of state ahead of elections on September 6 after Otto Perez Molina resigned on September 3.
Alejandro Maldonado is expected to govern until the new president is sworn in on January 14.
Guatemalans go to the polls on September 6 to take part in scheduled general elections.
Otto Perez Molina is constitutionally barred from seeking re-election.
Alejandro Maldonado had only been in the post of vice-president since mid-May, when his predecessor Roxana Baldetti resigned.
Roxana Baldetti is accused of involvement in the same corruption scheme that Otto Perez Molina is said to have masterminded. She is also being held in prison.
Otto Perez Molina’s resignation on September 3 and arrest are a huge victory for an unprecedented anti-corruption protest movement that had swelled in recent months, with regular marches in Guatemala’s major cities.
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