He told the AP news agency that it had been there long before the area was declared a sacred zone about 20 years ago.
But prominent monks in Dambulla say the mosque is illegally built on ground sacred to their religion.
On Friday the building was fire-bombed.
Buddhist leaders in Dambulla say they now intend to demolish 72 structures in the sacred area that they say are unauthorised, including the mosque and a Tamil Hindu temple.
A Dambulla monk told the BBC that the actions were necessary because Sri Lanka was “the only country to safeguard Buddhism”.