Route alignment options drawn up by HS2, the company set up by the Department for Transport to take forward its plans, included a connection from a new 250mph line from London to the West Coast line north of Preston.
This would have offered the best deal for passengers travelling north to Scotland as it would have cut journey times for Anglo-Scottish rail services, HS2 said.
But, in advice published on the DfT's website this week, it rejected this in favour of a junction south of Wigan to enable passengers from both Preston and Wigan to connect.
"Our key consideration here was that a connection further north would mean shorter journey times using HS2 (high speed rail) to Scotland; however, it would also mean that such trains would not be able to call at stations on the existing rail network between Bamfurlong and Brock," HS2 said.
The more northerly connection would have added £2 billion to the cost of building a high-speed rail network as it would have required a new interchange station to be built near Preston to maintain connections to Blackpool and other nearby stations.
The decision emerged amid a spat between the SNP and Scottish Labour over the lack of a concrete plan to bring high-speed rail to Scotland.
A spokesman for the Scottish Association for Public Transport condemned the route alignment favoured by the DfT, saying this ignored the benefits a line between Scotland and London would provide.