The plight of the two girls -- aged 13 and 15 -- came to light following a complaint by the man's wife, police said.
The man, a hotel employee, arrested near Kadurthuruthi in Kottayam district yesterday, has been charged under sections 376 (rape) and 377 (unnatural offences) of the IPC.
The mother, who had just returned from work, was informed by the crying girls about the assault after which she informed the police.
The incident comes close on the heels of a similar incident from Dharmadom in Kannur district where a 13-year-old girl had been sexually assaulted by her father, 15-year-old brother and an uncle for nearly two years. All the three have been arrested.
Kerala Home Minister Thiruvanchoor Radhakrishnan said in Thiruvananthapuram that police had been asked to conduct a thorough probe into both the cases and bring the culprits to book without delay.
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