Scottish ministers are coming under pressure to ensure trains travelling to one of Scotland's most popular cycling areas will be equipped to carry more than three bikes per carriage.
Correspondence between the Government's Transport Scotland arm and campaigners has revealed that cycle storage will be "the same as the rest of the rail network" when the new line opens in 2015.
This has dismayed cyclists and Borders business owners who believe thousands will want to take bikes with them and want the new line to be treated as a special case. Some have called for a dedicated bike carriage on weekend services, in what would be a first for Scotland.
The 30-mile Borders Railway will link Edinburgh with Tweedbank, south of Galashiels.
The area is popular with road cyclists and mountain bikers, regularly hosting stages of the Tour of Britain and an annual 10-day cycling festival, Tweedlove.
Glentress mountain biking centre, which attracts over 300,000 visitors per year, is at nearby Peebles and the rail line also runs close to Route 1 of the National Cycle Network.
The Federation of Small Businesses lobbied enterprise and tourism minister Fergus Ewing in a bid to ensure cyclists could make full use of the line.
But a reply on his behalf from Transport Scotland Borders Railway chief Lorna Davis said: "The cycle provision on the Borders Railway will be same as the rest of the rail network." She said the number of bicycles carried would be a decision for the train operator and "balance the needs of non-cyclists and cyclists".
Graham Bell, chairman of the Borders branch of the FSB, said: "The promotion of cycling in the form of mountain biking and cycle touring is a key plank of Scottish Borders Council's economic strategy and is vital to the area's tourism industry. We need to ensure the new route has appropriate facilities for cyclists.
He added: "A maximum of three bicycles per carriage wouldn't even allow one family with two children to travel together. Let's have a rethink and agree on reasonable provision to make the best of this fantastic investment."
A spokeswoman for healthy travelling charity Sustrans said: "The Scottish Borders have been successfully marketing themselves as a wonderful cycle touring destination and it is regrettable this new rail link will not be able to cater for increased volumes of cyclists."
The row comes as ministers prepare to consider bids for the next ScotRail franchise, due to start in March 2015.
A Transport Scotland spokesman said: "We recognise the importance of increasing integration of Scotland's transport networks, particularly cycling and the railways, as enhancing the travel experience is proven to help drive modal shift.
"Bidders for the next ScotRail franchise will be required to develop plans to improve rail's integration with the wider transport system, including improvements to facilities for cyclists."
The spokesman said cycle parking would be provided at all seven Borders Railway stations.
The £350 million railway will re-open a route closed in 1969. However it has proved controversial. Critics have called it a white elephant and Transport Scotland has admitted it will take 10 years to become profitable on the basis of projected passenger numbers.