The incident took place at Perumpullikkal in Pandalam on June 23 and the bodies were recovered from the well in a decomposed state today, they said.
The 33-year-old accused, Matthews, has been arrested, the police said.
The matter came to light this morning when relatives asked Matthews about his parents -- K M John (70) and Leelamma (63), and he told them they had gone for a prayer meeting.
However, neighbours grew suspicious as a foul smell emanated from the well near the residence of the Johns.
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But following the persisting odour, police were informed.
When Matthews was questioned, he admitted to having killed his parents after hitting them on the head over some property dispute, the police said.
Matthews is a BSc Nursing graduate but was jobless and had sent his wife and children to their home at Kottayam, they added.