The Strathspey Railway Company, which has been based at Aviemore since 1978, said it is having to use imported coal from as far away as Colombia.
It said this had “a much greater carbon footprint by sea and by road”.
Meanwhile, the Heritage Railway Association, the UK-wide trade association and professional support body, said the move "risks damaging the valuable contribution” that heritage railways and other sectors make to the tourism economy and cultural heritage of Scotland.
The Scottish Government has said its “preferred policy position is no support for coal extraction in Scotland”.
Powers over coal exploitation are reserved to the UK Government, with the Coal Authority responsible for licensing coal mining activity. However, planning policy and determinations are devolved to the Scottish Government, meaning it can effectively block new developments.
There are no operational coal mines in Scotland, and the last coal power station closed in 2016.
In January, the Coal Authority awarded a conditional coal mining licence for an area extending into Dumfries and Galloway.
Responding to a Government call for evidence on coal extraction, the Heritage Railway Association said: “The basic supposition that this call for evidence is based upon, is that permanently ending coal extraction in Scotland will reduce emissions. We believe this is seriously flawed and risks damaging the valuable contribution that heritage railways and the wider coal using heritage sectors (including road steam vehicles, maritime steam vessels, historic homes, blacksmiths and industrial museums) make to the tourism economy and cultural heritage of Scotland.”
The association said removing the opportunities “for low-volume extraction of high-quality coal in the UK is at best off-shoring emissions and at worst, actively increasing them”.
The body said the heritage rail sector welcomes 13 million visitors and generates £600 million for the economy every year across the UK, adding: “The key role that railway heritage plays in Scottish cultural identity has been readily identified on the global stage. A number of Hollywood blockbusters have chosen steam locomotives to feature as a key identifier of the nation – this is, of course, exemplified in the appearances of the Hogwarts Express on Glenfinnan Viaduct in the Harry Potter films.”
The Strathspey Railway Company said it was able to obtain suitable coal from Scottish sources at relatively stable prices until this year.
The company said: “Currently we are having to use imported coal from as far away as Colombia, which costs three times as much as the Scottish product and has a much greater carbon footprint by sea and by road, from an English port, to reach Aviemore.
"In summary this is seriously detrimental to our business, future investment and employment levels.
"A Scottish source of coal is absolutely required to avoid these expensive and environmentally damaging imports.”
A Government spokesman said: "The Scottish Government's preferred policy position is no support for coal extraction in Scotland. We have been clear than unlimited extraction of fossil fuels is not consistent with our climate obligations.
"This position is supported by the UK and Scottish Government’s statutory advisers on climate change. We recognise the challenges involved in shifting away from fossil fuels for some sectors and continue to work with them to help find solutions.”