It followed speculation that Transport Scotland, which is in charge of overseeing the much vaunted £295 million building project, is planning to reduce the length of crossing loops on the single line track in an attempt to cut costs.
However, the Campaign for Borders Rail warned that would increase journey times between Tweedbank and Edinburgh, beyond the 55 minute maximum currently planned, and end up costing more in the long term.
And now the local lobby group, which was setup to campaign for the restoration of the region's rail links, has written to the Scottish Transport Minister, Keith Brown, to seek assurances over the line's future.
They have also reiterated their plea for the two platforms proposed at the planned terminus in Tweedbank be extended, from the current six-coach specification for standard ScotRail services to 10 or 11 coaches in length, to accommodate so-called tourist trains which they claim could generate an extra half a million pounds for the local economy each year.
In his letter to the Transport Minister, Lorne Anton, chair of Campaign for Borders Rail, said: "The Campaign for Borders Rail views with increasing concern the substantial cut backs in the EGIP Programme for improving the rail service between Edinburgh and Glasgow.
"Of even greater concern to the Campaign are rumours of possible Transport Scotland proposals for reductions in the crossing loop lengths on the Borders Railway, which would result in increased journey times between the Borders and the Capital. Longer train journey times will reduce patronage and deter a modal shift by motorists from car to train.
"Taken in conjunction with the possibility that Tweedbank Station may not be capable of handling full-length passenger charter trains, with the resultant loss of economic benefits to the Borders and Midlothian, the Campaign is seriously concerned that the rail project will not be allowed to realise its full economic, social and environmental potential.
"It has been suggested that there would be later - post opening - opportunities to put right initial deficiencies in the specification for the railway, but implementing enhancements in an operational railway is much more expensive than doing the job properly at the outset.
"We urge the Scottish Government to provide early re-assurance that the journey time from Tweedbank to Edinburgh , and from Edinburgh to Tweedbank, will be the maximum 55minutes laid down in the specification in 2009, and that a way will be found to properly accommodate the tourist charter train market on the Borders Railway."
Earlier this year, a multi-million pound contract was awarded to develop the designs of the new rail route between Edinburgh and the Borders. Network Rail, the authority responsible for the country's rail network, announced it has appointed BAM Nuttall to assist in the delivery of the Borders Railway. It is hoped the first trains will run on the line by late 2014.
Mr Anton said: "The Campaign for Borders Rail remain totally supportive of all Government Departments and Agencies, both national and local, who are striving to deliver the best possible Borders Railway by 2014."
Transport Scotland this week insisted the speculation that the brakes were being put on plans to reintroduce train services to the Borders was way off track. A spokesperson said: "These claims are inaccurate. Bringing benefits for local communities and businesses in Midlothian and the Borders remains the key consideration in our work with Network Rail towards delivery of this project.
"Investigations undertaken during the Parliamentary process indicated that scheduled passenger services were the only viable option at that time. However, with the use of additional stewarding procedures, it would be possible to run charter trains to Tweedbank, without any additional costs or delay to the project."
And they added: "As we progress the detailed design our focus continues to be on journey time efficiency."