The train operator brought in the ban, which includes lawfully owned guns, after a licensed firearm was left unattended on a train this year.
But the British Association for Shooting and Conservation (BASC) said it posed a problem for people travelling to sporting estates.
It said the ban could have a "negative impact" on the Glorious Twelfth.
Traditionally, the first day of the grouse shooting season is 12 August.
BASC has raised its concerns in letters to Scottish government ministers.
Peter Glenser, the association's chairman, said:  "ScotRail has imposed a ban which will damage Scotland's reputation as an iconic fieldsports destination.
"ScotRail claims it is Scotland's railway but it is striking at the heart of rural businesses and communities which rely on the estimated Â£155m injected each year into the country's economy by country sports tourism.
"BASC understands that this outright ban is a result of a single incident of a shotgun being left on a train.
"Considering the millions of miles travelled safely with shotguns and firearms each year, this decision looks like a disproportionate, knee-jerk response."
ScotRail said the decision to introduce the ban was made for safety reasons.
David Lister, ScotRail Alliance's safety and sustainability director, said: "The safety and security of our customers and staff is our number one priority.
"Following an incident earlier in the year, when a customer left a firearm unattended on a train, we reviewed our policy and decided that the best way to keep our customers and staff safe is to ban all firearms on ScotRail services.
"We are confident that this is a decision that will have the support of the vast majority of staff and customers."
The UK's largest shooting organisation has asked ScotRail to lift its ban on the transportation of all firearms.