Staff have been told to bring their own mugs for takeaway hot drinks in cafes and canteens at offices including St Andrew’s House and Victoria Quay in Edinburgh and Glasgow’s Atlantic Quay.
Ceramic mugs will be provided for those sitting in after the change is implemented on June 4.
The government said the move would stop 450,000 cups from being thrown away each year.
Scotland’s Environment Secretary Roseanna Cunningham said: “The Scottish Government is determined to lead by example when it comes to tackling the scourge of plastic littering our countryside and polluting our seas.
“By removing single-use coffee cups from our main buildings, we will prevent 450,000 cups from being thrown away every year. That’s enough cups to cover the distance between Edinburgh and Dundee.
“We support the EU’s vision to reduce single-use plastics as far as possible and ensure any single-use plastics are easily recyclable by 2030.
“We are currently considering what other single-use items can be reduced and removed from Scottish Government buildings later this year.”
The government has appointed an expert panel to look at further action on disposable cups and plastic straws in Scotland.
The panel is being led by electoral commissioner Dame Sue Bruce, with representatives from retail, the waste and chemical industries, the public sector and academia.