Police said 23-year-old Veerasami was picked up from Udumalpet in nearby Tirupur district yesterday based on a tip-off and after preliminary interrogation he was arrested this evening.
Police said there was already a rape case against Veerasami some months ago, when he allegedly sexually assaulted a beggar-woman near Pollachi.
Meanwhile, based on a complaint from the Social Welfare department, police arrested the hostel warden, Sureshkumar, for running the hostel without valid licence for the last 20 years and keeping the inmates without adequate security, they said.
Police are also on the lookout for one Bhagyanathan, a worker in the hostel which is run by the Tamil Evangelical Lutheran Church.
Some officials from TELC, Tiruchirapalli, have come to Pollachi to take stock of the situation, police said.
The girls, aged 10 and 11 and inmates of the hostel in Pollachi, about 35 km from here, were bodily lifted and raped on the terrace of an adjacent building reportedly at knifepoint by two persons who approached them in the wee hours of June 12 on the pretext of asking for water.
The girls were rescued and admitted to Pollachi Government Hospital by police, after the inmates, one of whom was thrashed by the rapists, informed hostel management, who in turn alerted police.
Meanwhile, police denied permission to Arjun Sampath, president, Hindu Makkal Katchi to visit the hostel and the girls in the hospital.