The women were Wednesday abducted from the madrassa by four unidentified men who raped them and dropped them off at the seminary. Police filed a complaint Friday night and arrested four people for the crime.
However, the activists, mostly from the Congress and the Communist Party of India-Marxist (CPI-M), accused police of indifference and inaction against the "real culprits".
"The suspects booked are ordinary rickshaw pullers being framed to protect the real culprits," said CPI-M leader Subhashini Ali.
Allahabad district magistrate Amrit Abhijat denied the charge.
"People are trying to politicise the crime. We have already taken action in the matter," Abhijat told IANS.
Ali and Congress leader Rita Bahuguna-Joshi led the protest rally that turned violent when a major thoroughfare was blocked and some activists hurled stones at the Kareli police station on the outskirts of Allahabad, about 200 km from Uttar Pradesh capital Lucknow.