Prajapati, along with six others, have been charged with gangraping a woman and molesting her minor daughter in 2014.
An FIR was lodged against Prajapati on February 17 after a directive of the Supreme Court, and the former minister had been on the run since.
The police arrested three of Prajapati’s accomplices, including his two sons, on Tuesday. They have been booked for giving shelter to the accused.
The police had earlier issued a non-bailable warrant against Prajapati, and his passport was impounded to stop him from fleeing the country.