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The government has scrapped plans to build a new £3bn rail link between HS2 and the West Coast Main Line.
The 13-mile (21km) Golborne Link in Greater Manchester will no longer be built, even though it was included in the Integrated Rail Plan for transforming the Midlands and North.
The Railway Industry Association, Rail Freight Group and High Speed Rail Group fear a "bottleneck" will be the result.
The government said it would study alternative plans.
The Golborne Link would have branched off the the high-speed line between Crewe and Manchester and cut through Trafford to join the West Coast Mainline south of Wigan.
HS2 Minister Andrew Stephenson said the government would now explore how HS2 trains could best get to and from Scotland.
The timing of the announcement, just 30 minutes before the outcome of the confidence vote in Boris Johnson's leadership of the Conservative Party was revealed, has been criticised.
'Essential'
In their joint statement, the three railway industry bodies said: "It is hugely disappointing to discover that, on a day when much political attention was focused elsewhere, the government confirmed that the Golborne Link is to be removed from the HS2 project.
"Only six months ago, the Golborne Link was included in the Integrated Rail Plan, as well as the HS2 Phase 2b Bill.
"The link has been provided for in the budget for HS2 and is needed to allow adequate capacity on the national rail network to fulfil its vital function of handling the nation's longer distance movements of both passengers and freight.
"Without this connection, a bottleneck will be created north of Crewe on the West Coast Main Line, which in turn will negatively impact outcomes for passengers, decarbonisation and levelling up."
They said it was now "absolutely essential" for the government to "confirm as quickly as possible how ministers intend to protect the benefits of HS2 investment.
"Such an important, strategic question of how HS2 services connect into Scotland cannot be left open or uncertain," the statement added.
The announcement comes six months after the government dropped its plan to extend HS2 to Leeds.
Construction on the Golborne Link had been due to start in the early 2030s, with the connection expected to open towards the end of that decade or in the early 2040s.
Mr Stephenson said: "HS2 is a once-in-a-lifetime project that will transform travel across the entire UK as we know it and serve millions of people for hundreds of years to come, and it's absolutely vital that we get this right from the outset.
"Removing this link is about ensuring that we've left no stone unturned when it comes to working with our Scottish counterparts to find a solution that will best serve the great people of Scotland."
Plans for the Golborne Link faced fierce criticism from MPs, councillors and local residents.
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