The message comes after crew members reported numerous incidents where used tissues were left on the seats and tables in train carriages.
The issue has been more noticeable since the coronavirus pandemic.
A spokesman for the train company said: “We're seeing numerous reports from crews of dirty tissues being left on tables and seats.
“This isn't fair on anyone.
“Our Train Presentation teams regularly clean our bins - inside and out - so please use them.”
“Used tissues belong in the bin, don't leave them for someone else to find and deal with.
“Catch coughs and sneezes in a tissue. Bin it immediately. Wash your hands with soap and water for 20 seconds.
“Catch it. Bin it. Kill it.”
In response Traffic Scotland posted on twitter: “Come on folks, if you have to use public transport as a necessity please dont be doing things like this
“Its careless, reckless and dangerous to those Key Workers who are keeping the country running at the moment
“Pop those used tissues in the bin where they belong.”
The train company has recently been under fire from members of the public after pictures were shared on social media of people crammed together on ScotRail services at peak times.
But David Lister, ScotRail Sustainability and Safety Assurance Director, said people have been warned by the government they should only use transport if it is essential.
He said trains are still available but to provide a critical service for key workers.
He added: “This is an unprecedented challenge on Scotland’s Railway and the revision of the timetable is very clearly aimed at providing a critical service for the key workers across the country.
“The advice for people not to travel unless absolutely necessary could not be clearer, and we urge people to follow that guidance and help us to deliver this essential service.
“The railway has an important role to play during this crisis and people need to take responsibility to follow the expert advice.”
ScotRail has recently reduced trains running amid the coronavirus outbreak.
In doing so, staff have had extra time between services to make sure the trains are extra clean before using.
Today the company pledged to add more services for key workers if needed and insisted overcrowding has been cut.
Those travelling plummeted by 80 per cent and 70 per cent on Monday compared to normal.