The deceased has been identified as Mariappan (50), a worker at the godown, the police said.
The godown is located on a busy stretch at Mettualipatti on the outskirts of Manaparai town.
People rushed out from their houses on hearing the deafening sound and found three persons with bleeding injuries and rushed them to the hospital.
One person was found dead with his body blown to pieces, the police said.
The police suspect some explosive materials could have been stored in the godown and it would have exploded.