John Cridland, who until last month was chairman of Transport for the North (TfN), said a proposed overhaul of timetables on the East Coast Mainline were too focused on journeys between key cities such as Newcastle and London.
And he warned that if the changes were allowed to go ahead, it could damage efforts to revitalise neglected parts of the North East.
He said: “I am concerned that the East Coast Mainline consultation seems to be very focused on fast trains from Edinburgh to London.
“That’s important, it’s connecting two really critical world class cities, but it’s not sufficient.
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“And if we do that at the expense of east-west links I think it will be weakening [the government’s] levelling agenda, not strengthening it.”
Morpeth and Berwick, where Mr Cridland also lives, are expected to be two of the North East’s biggest losers if the proposals go ahead.
Northumberland faces seeing 24 services a day cut from timetables under plans being considered by LNER and the other operators on the East Coast Mainline.
Morpeth would take the biggest hit, with LNER removing all stops for the town between 8am to 8pm, Monday to Saturday
Berwick would see trains to London, York, Darlington, Newcastle and Edinburgh cut to just one every two hours.
Transport chiefs have suggested other operators could fill the gaps in timetables with new options.
But in recent weeks campaigners have started to predict rail chiefs are preparing to return to the drawing board, following an outcry over the proposals.
Mr Cridland added: “Transport planners spend a lot of time looking at what’s best for northern people, but we shouldn’t focus on speed of trains and speed of journeys in isolation.
“The LNER service is excellent and I want to be able to use it more.
“Berwick is a regional centre for north Northumberland, which is a long way from Newcastle, and for the Scottish Borders, which is a long way from Edinburgh.
“If you don’t stop at Berwick, you can run the train five minutes faster, but – and I admit I live in Berwick – is the loss to thousands of people in north Northumberland and thousands of people in the Scottish Borders justified by getting to Edinburgh five minutes earlier?
“I think it’s just the wrong call.”
LNER’s eight-week public consultation on the proposed changes ended on August 5.
A spokesman for the operator said: “Our consultation provided the opportunity to share and discuss plans for thousands more seats between London, York and Newcastle and significantly improved journey times between London, York, Newcastle and Edinburgh.
“We thank everyone who submitted a response and took part in a briefing session.
“We are currently reviewing the responses received and will provide an update in due course.”
It is not yet known when that update will be provided.