The incident occurred past midnight when the two accused came to the hostel run by a church and asked for some water. When the girls, aged 10 and 11, fetched water for the duo, they pulled them by their hands, police said.
A boy in the hostel witnessed the incident and questioned the men, but was thrashed by the duo, who then forcibly took away the girls to a nearby complex and raped them, they said.
The victims, were admitted to a Government Hospital in Pollachi, about 35 kms from here, with severe bleeding and injuries, police said.
Sub Collector Rashmi Siddarth, who visited the girls at the hospital, reportedly fainted after witnessing their plight and was administered first aid by doctors there.
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Davidson Devashirvatham, IG, West Zone and Sudhakar, Rural SP, who are conducting an inquiry, said they have received 'some clues' and would soon bring the culprits to book.
They alleged that there was no proper security in the hostel, which was reportedly being run without any licence.
The hostel accommodates 17 boys and three girls.
Police said some persons had come to the hostel a couple of days back, asked for water and attempted to catch a girl by her hand. However, other students managed to send them out of the hostel campus.