Heritage New Zealand spokesman John O'Hare was reluctant to comment on either drone incident in June other than to say drones bring their own issues, including potential damage to historic buildings and injury to others.
Mr O'Hare said HNZ is developing a policy and processes for use of drones at its historic properties and will be making that publicly available.
The glass windows on both buildings are vintage and known to be delicate.
The corners of the Stone Store building are sandstone and soft, and the concern from locals and volunteers who work at the Mission Station is that drones could seriously damage irreplaceable parts of both structures.
The number of recorded drone "incidents" in New Zealand has risen in line with popular use.
In 2010 only one incident was reported to the CAA but by 2013 the figure had climbed to 121. Since the new rules were introduced the number of incidents recorded so far is 87.
Jessica Jennings, communications adviser with CAA, said drone operators flying in public spaces usually obtain permission from local councils who set their own rules and some councils ban drone flying over public places altogether.
Ms Jennings said people are urged to report incidents to CAA on 0508 4SAFETY (0508 472 338). Find out more at www.airshare.co.nz