The train operator said offenders and also people who leave used chewing gum on the seats are costing the firm the huge sum in Scottish Government penalties.
ScotRail also said it had to fix more than 350 seats last month, which included nearly 100 damaged by discarded gum.
The company has launched a campaign to tackle the problem.
Almost half of all ScotRail penalties were directly attributed to what were called 'seat failures' in the monitoring scheme by Transport Scotland's Service Quality Incentive Regime.
Penalties for the last 12 months to June totalled £372,849, which was down 16.5% from the previous year.
However, seat penalties cost £173,450 in the same period, which was up 160% from the £66,960 in the year before.
More than half of these penalties – £90,194 – were attributed to damage caused by passengers, mainly by people putting feet on seats
ScotRail's new campaign is aimed at encouraging people to show respect for other passengers and property.
It includes promotional events at five ScotRail stations, and new posters and announcements on trains.
They will show 'Neat Seats' information stands, featuring giveaways such as 'gum bins' at stations, which will include Central, High Street and Partick, Glasgow, and Kilwinning, Ayrshire.
Steve Montgomery, ScotRail's managing director, said: "Unfortunately, the amount of damage caused to train seats is growing.
Everyone deserves a clean seat, and this campaign is to make our trains an even more pleasant and comfortable way to travel."
The campaign has also been backed by environmental charity, Keep Scotland Beautiful, which has campaigned against litter and waste for more than 40 years.
Chief executive Derek Robertson said: "We are delighted to support all ScotRail campaigns that encourage people to show respect for their environment.
"The campaign will raise public awareness of the growing problems caused by passengers' feet on seats.
"It is a key component in changing the behaviour of a minority of railway users who show a lack of consideration for fellow passengers."