Arran Brewery bought a former primary school in Dreghorn two years ago with a view to converting it into a production centre for Japanese rice wine.
But a string of break-ins have led company bosses to consider pulling the plug on the entire project.
On Sunday, £5,000 worth of damage was caused by vandals to equipment in the building.
It followed several thefts from the school in late 2014.
Arran’s board of directors will reportedly meet later this week to decide on the best way forward for the project.
There are concerns HM Revenue & Customs will not grant a license to hold duty-free stock at Dreghorn if the company cannot secure the site.
“We are having crisis meetings to decide what we will do, but at the moment many of our board members just want to pull the plug on the site and move somewhere else,” managing director Gerald Michaluk told The Herald.
“We cannot make this site look a prisoner-of-war camp with security cameras everywhere and barbed wire.
“It has to be a place that people enjoy walking around.
“These are thug-like attacks, using chisels and screwdrivers and smashing or kick in doors with no apparent fear of being observed by our CCTV camera.
“The damage caused and items stolen is heart-breaking.”
Arran first announced its plans for a sake brewery in Ayrshire in March 2014.
Speaking at the time, Michaluk said: “It may not at first appear there is a connection between Dreghorn, near Kilmarnock, and Japan but there is.
“In Japan you will find a small piece of Scotland in the form of a church which once graced Dreghorn but which was dismantled and rebuild in Tokyo.
“As well as the sake brewery which will almost exclusively export its sake to Japan, there will be a research and development centre and a brewing and distilling training school subject of course to licensing.
“We have been making sake on a very small, almost domestic, scale and are now ready to build a sizable facility.”