The incident occurred during the "Kazhcha seeveli", a daily procession of caparisoned elephants.
A woman also suffered minor injuries as panic stricken devotees ran helter-skelter.
The mahout was admitted to a hospital in Thrissur, where he succumbed to the injuries in the evening, the police said.
The incident took place at around 7 am, when the elephants were lined up at the temple, with one of the tuskers carrying the idol of Lord Krishna, they added.
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Temple sources said the idol was taken away from the elephant carrying it when the incident took place.
The jumbos ran in different directions and one of them attackedits mahout, seriously injuring him, the police said.
Subsequently, all the three animals were brought under control.
There was a heavy rush of devotees at the temple, today being a Sunday, and also on account of Sabarimala pilgrims visiting the shrine.