Historical and epigraphical records confirm that the temple existed well before the French East India Company established its trading post at Pondicherry under François Martin in 1673. In the late 17th and 18th centuries, during periods of colonial religious friction under Governor Joseph François Dupleix and French Catholic authorities, several attempts were made to remove the Hindu shrine and relocate the stone idol into the sea.
Local oral tradition and historical diaries (notably those of court diarist Ananda Ranga Pillai) record that despite the stone idol being thrown into the Bay of Bengal on multiple occasions, it was repeatedly recovered and reinstated in the sanctum by devoted Tamil residents. Acknowledging the unyielding devotion of the populace, the French administration subsequently ceased interference, and European merchants and French officials frequently sought the blessings of Manakula Vinayagar before embarking on maritime voyages.
