As per the storeroom's licence, only 15 kg can be stored, police said.
The Mandala-Makaravilakku festival season is currently on at the temple.
The gunpowder was recovered from the storeroom near the Mallikapuram shrine at Sannidhanam (temple complex), police said.
It was to be used for the preparation of 'Kathina Vedi', an offering for the presiding deity at the temple.
Police found that the room lacked the requisite safety measures to keep the explosive material.
Thousands of pilgrims are visiting the hillock shrine every day to catch a glimpse of Lord Ayyappa and offer prayers.
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