Ancient history according to the Mahavamsa chronicles and the Tamil Buddhist epic Manimekalai mentions a gem-studded throne and a stone with the Buddha’s footprint at the island Nainativu, (also known as Nagadeepa) which pilgrims from India visited.

[2][3] The site is known as the place where Lord Buddha came during his second visit to Sri Lanka, after five years of attaining Enlightenment, to intervene and mediate in settling a dispute between two Naga Kings, Chulodara and Mahodara over the possession of a gem-studded throne.

During the 1958 riots[6] Tamil mobs that came from boats destroyed parts of the temple including a gold plated Buddha statue gifted from Burma which was beheaded and its arms removed and thrown to the sea and stupa which was blown up using dynamite.

[7] The government censored the incident at the orders of Governor-General Sir Oliver Goonetilleke who feared that the news would lead to further violence and restored the temple in secrets and the then head priest Rajakeeya Panditha Brahmanawatte Dhammakithi Tissa Mahanayaka Thera cooperated considering it an 'exercise of deception' in the interest of humanity.

The explosion was set off prematurely due to a navy patrol and the enraged naval personnel nearly went on a shooting spree that was averted by Dhammakithi thera who accosted them and calmed the soldiers who then returned to their barracks.