In Dwaparayuga the pandavas lost everything to kauravas in the gambling game. They had to go into exile for 13 years in forest. During that time according to Sri Vedavyasa's advice Arjuna started practicing Thapasya to get arrows with divine power from Sri Parameswara. Lord Siva appeared before Arjuna in the form of a tribesman (vedan) accompained by Sri Parvathi and the Bhutaganas. He was pleased by Arjuna's devotion and blessed him with the powerful Pasupathasthra for his victory over the enemies. This avathara of Lord Siva popularly known as Vettekkaran is the main diety of Ottapalam Sri Vettekkaran Temple.
This Kavu is believed to have a history of more than 850 years. Brahmin population was predominant in the locality during ancient period. A Brahmin from one of the families became a sanyasi and left the village. This family later became childless and was much concerned about their future. The sanyasi who came back to visit the place advised the family members to worship Kirathamoorthi. Their prayers were successful. They started worshipping Kiratha moorthi as a family deity.
About 300 years back there were continuous conflicts between this family and the naduvazhis of Zamorin. Many Brahmins were killed. Zamorin dynasty managed the temple. With the decline of Zamorin dynasty, the temple management was entrusted to ‘Nambrath’ family who started worshipping Kirathamoorthi as well as Bhagavathy. The temple was managed by one Mr. Chappunni Nair for a long period. He handed over the temple management to the ‘Elavally' family. The Elavally family gave the present form to the temple.