The Scottish Government said it was “unacceptable” that LNER had decided to remove the need for people to be 1m apart on all cross-border trains from Monday onwards.
LNER said it would be operating its services under “English guidance”, which means that passengers can now be seated next to each other even if their journey begins in Scotland.
This is despite the rules in Scotland being different to England, with 1m social distancing still in place in all indoor public spaces including public transport.
However, the train operator on Monday night said it was “reviewing” the policy following the backlash, signalling that a possible U-turn may be imminent.
LNER is also asking customers to continue to wear face coverings on its trains, despite this only being a legal requirement in Scotland and not in England.
The social distancing policy was attacked by Michael Matheson, Scotland’s transport secretary, who described it as “unacceptable”.
“LNER services operating in Scotland should comply with the Scottish Government public health guidance,” he said.
"I’ve asked Transport Scotland officials to address this point with LNER.”
Angus Robertson, Scotland’s constitution secretary and another member of Nicola Sturgeon’s Cabinet, also criticised the decision.
“LNER is a train company owned by the UK Government,” he said. “Is it still maintaining that when it operates in Scotland it is going to disregard Scottish public health and safety coronavirus rules?
“This is as tenable as Boris Johnson's exemption from social distancing regulations.”
Twitter user Tamsin Russell said she was “completely confused and dumfounded” by LNER’s policy on the issue and challenged the company to justify it.
Responding to her, LNER said: “We have made the decision to operate under English guidance, with regards to social distancing on cross border services, to provide consistency to customers. Therefore, customers may be seated next to each other when travelling from July 19 onwards.”
A spokesman for Transport Scotland said: “The law is clear that social distancing is required on public transport, including on cross border services.
“It is our expectation that operators providing a public transport service in Scotland to comply with the law as far as is reasonably practical and inform passengers.”
The spokesman said the issued had been “flagged” with LNER in advance of the rules changing on Monday, and the company was now issuing “inaccurate advice”.
He said: “We are now discussing this issue again with LNER as a matter of urgency to ensure an approach consistent with Scottish restrictions.”
An LNER spokesman said: “We are reviewing our approach to social distancing on board our Anglo-Scot services. The safety of our customers and colleagues remains our top priority and we will provide an update in due course.
“We are continuing to provide an enhanced cleaning programme on board our trains and at our stations as well as reminding customers to wear a face mask, unless exempt.
“We are also using our reservation system to prevent overcrowding and our website to continue to inform customers which are our least busy and busier services, to enable people to plan ahead and travel in confidence.”