The 64-year old left the court in Guatemala City on Thursday under heavy police guard and was taken to a military prison in the capital.
Despite denying any wrongdoing, Congress, on Tuesday, stripped him of his immunity from prosecution which opened the way for criminal charges to be brought against him.
He has denied any wrongdoing.
The vice-president was sworn in as interim head of state ahead of elections this Sunday after Mr Perez Molina resigned on Thursday.
Alejandro Maldonado is expected to govern until the new president is sworn in on 14 January.
Mr Maldonado has only been in the post since mid-May, when his predecessor Roxana Baldetti resigned.
Ms Baldetti is accused of involvement in the same corruption scheme that Mr Perez Molina is said to have masterminded and she is also being held in prison..
