The temple was built in the 11th century CE by the Chola ruler Kulothunga Chola-I and later expanded in 1336 by the Vijayanagara emperors, boasts a rich history spanning over a millennium.

The temple is known for its Swayambhu idol of Lord Ganesha, a narrative firmly ingrained in local history.

The story involves three brothers with disabilities: one could not see, one could not speak, and the other could not hear. They lived near the village and supported themselves by cultivating a small plot of land that their parents had given them. For irrigation, they relied on a well located on their land. One day, it seemed the well had run dry, prompting the brothers to dig deeper in their search for water. While excavating, the shovel hit a dark stone, and to their surprise, blood began to seep out of it, turning the surrounding water red. Inexplicably, the blood-infused water miraculously healed the brothers' disabilities.

The news of this wonderful event quickly spread to many people. The people began digging around the well in an attempt to extract the miraculous water. As they dug, they discovered a figure of Lord Vinayaka that kept getting bigger, leaving them surprised with joy. In response to this amazing event, people from nearby towns came to offer coconuts and participate in rituals. The holy water from the well came out and formed a stream that spanned 1.25 acres. The place was later called "Kanipakam," which comes from the Tamil words "kani" which means "an acer land" and "parakam" which means "flowing water".

The well still houses the idol of Lord Vinayaka, from which water flows continuously. It is believed that the water flows into the holy Bahuda River. The idol is remarkably well known for its ongoing growth. Approximately fifty years ago, a devotee named Lakshmamma gifted a silver kavacham (protective armor) to the deity. Notably, the kavacham no longer fits, underscoring this unique phenomenon.