The logo was used as the backdrop for the First Minister’s Covid briefings throughout the pandemic, with a navy screen being overlayed with white lettering and a white inverted saltire.
This flag is also used by the Russian navy and is the flag of St Andrew.
The Times reported the logo would no longer be used for Covid briefings.
The Government confirmed, due to the Russian invasion of Ukraine, the logo would no longer be used.
A spokesperson said: “The white with blue Saltire version of the Scottish Government logo is part of the organisation's approved branding toolkit.
"Given the ongoing situation in Ukraine, the Scottish Government will no longer be using this version of the logo.”
The design has been used as the Russian navy flag since the early 18th century following orders from Peter the Great.
St Andrew is a patron saint of Russia as well as Scotland, with the design ditched in 1918 and reinstated following the establishment of the Russian federation in 1992.
It was later made the banner of the Russian navy in 2000 by Vladimir Putin.
A Scottish Conservative spokesperson said it was the “right decision”, which avoided an “embarrassing situation”.
They said: “That would have been an entirely inappropriate scenario given the appalling actions by Vladimir Putin, so we’re pleased to hear that this logo won’t see the light of day any longer.”