Emergency services were called at around 1am to reports of a fire at the observatory between Dalmellington and Loch Doon.
A joint investigation by Police Scotland and the Scottish Fire and Rescue Service is being carried out, however the blaze is being treated as suspicious.
Detective Constable Steven Grey said: "The observatory is run by a charity organisation and the financial impact and damage caused is extremely significant.
"It is vital we establish the full circumstances surrounding what happened.
"The observatory is in a remote location and I would like to speak to anyone who may have been in the area on Tuesday night, into Wednesday morning.
"I would also urge any motorists with dashcams who were travelling through at the time to please check their footage in case they have captured anything which could be of relevance.”
If you have any information you should contact Police Scotland on 101 quoting incident number 0293 of Wednesday, June 23.
Elena Whitham, the SNP MSP for Carrick, Cumnock and Doon Valley, said on Facebook: "I'm receiving reports that the Scottish Dark Sky Observatory at Loch Doon suffered a fire in the early hours of this morning.
"Thank you to Police Scotland and Scottish Fire and Rescue Service who attended the incident and are, I understand, investigating the cause of the fire.
"I will be speaking with colleagues later today to seek more information and see what needs to be done to save this wonderful asset for the Doon Valley and wider South West Scotland."