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Labour’s crackdown on some of the last privately run rail routes threatens to extinguish vital train services to poorly connected towns and cities, operators have warned.

So-called open-access services will “wither on the vine” after new restrictions were imposed by Heidi Alexander, the Transport Secretary, according to an industry lobby group.

Open-access operators – which, unlike franchises such as LNER, are not paid by the Government to run services and instead make their money only from passenger fares – will remain in private hands after Labour has nationalised the rest of the industry.

However, Ms Alexander wrote to the rail regulator on Monday advising it to adopt a more rigorous stance on open access and warning that she planned to modify official guidance for approving applications.

Rail Partners, which represents nine private train companies, said Ms Alexander’s instructions to Declan Collier, the chairman of the Office of Rail and Road (ORR), called the Government’s commitment to the model into question.

Andy Bagnall, the chief executive of the trade group, said the letter sends a “worrying signal” and “suggests that the bar for new open access applications is being made harder to clear”.

He said: “If the Government doesn’t make a positive choice to grow the sector through adequate safeguards and a fairly adjudicated application process, it will effectively be creating the conditions for existing operators to wither on the vine.”

Mr Bagnall said the past 18 months had been a breakthrough period for open access, with its role in creating travel opportunities for underserved communities and fostering fare competition increasingly recognised.

Sir Keir Starmer’s visit to the Hitachi plant in County Durham to support a deal to make new trains for FirstGroup’s open access services was viewed as particularly positive, he said.

Yet following Ms Alexander’s intervention he warned that it is “unclear whether the new Government is a champion of open access operators or it is simply tolerating them as part of the system that is too costly to nationalise”.

Ms Bagnall urged the Government to “signpost the future direction of travel for open access operators.”

In her letter to the ORR, the Transport Secretary said she accepted that open access routes can be beneficial in opening up new markets.

However, she said the regulator must be mindful of whether that is outweighed by other impacts, such as the abstraction of revenue from other operators, which even under existing contracts would otherwise have gone to the Exchequer.