With this, six persons named in the FIR against the 49-year-old SP leader have been picked up.
"Today's arrests were made from Hazratganj area in central Lucknow," IG (Lucknow) A Satish Ganesh told PTI.
Earlier Prajapati's two aides were arrested from Noida near Jewar on the Yamuna Expressway on March 7.
The minister's security guard Chandrapal was arrested on March 6 near Lucknow Police lines.
Prajapati was booked on a Supreme Court directive and an FIR was lodged on February 17 against the minister and six others for allegedly gang-raping a woman and alleged attempt to rape her minor daughter.
The apex court had asked the UP Police to submit an action taken report regarding the incidents in eight weeks. UP Police plans to attached two properties of the minister in Lucknow and one in Amethi, his assembly constituency, to force him to surrender, SSP Lucknow Manzil Saini told PTI.
A Look Out notice has already been issued against him as also a Non-Bailable Warrant. His passport too has been impounded.
Earlier, airports across the country were alerted about the possibility of Prajapati trying to flee the country. In the just-concluded Assembly elections in Uttar Pradesh, Prajapati lost from Amethi, the seat he held, to BJP.