The victims were staying at 'Balbhavan' in Meenangadi where the priest was working, a police official said.
Fr Saji Joseph, who was allegedly sexually assaulting the boy's since March 2015, was arrested following complaints from children's relatives, the offcial said.
He was absconding for the past three days and was arrested from Thamarassery near here yesterday. He hid at various places, including Mangaluru, they said.
The official said Joseph has been charged under section 377 (unanatural offences) of the Indian Penal Code, and relevant provisions of the Protection of Children from Sexual Offences Act (POCSO) and the Juvenile Justice (care and protection of children) Act.
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The priest had gone missing after relatives of the children complained to the police. Childline authorities were also informed.
The priest hails from Kottiyoor in Kannur district.
On February 28, a Catholic priest had been arrested on the charge of sexually abusing a minor girl who later gave birth to a child.
The 48-year-old priest Robin Vadakkancheril was a vicar at the St Sebastian's Church in Kottiyoor.
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