Modi arrived in Kochi late Friday night. He flew to the temple town in a helicopter from the Cochin Naval base.
According to authorities, Modi is expected to be in the temple for an hour where he will be offering various items including ghee, a special variety of red plantain (kathali), a 'tulabharam' with lotus flowers, among other things.
Modi had visited the temple in 2008 soon after he became the Chief Minister of Gujarat for a second time.
After an hour-long 'darshan' at the temple, the prime minister will address a party meeting Abhinandan Sabha being organised by the BJP Kerala State committee.
This will be Modi's first public meeting after assuming the chair of the prime minister for a second consecutive term.