The line is due to stop at Leeds and Manchester but Tory-LibDem ministers will later this week announce a new study on how to take it to Glasgow and Edinburgh. It is expected to look at how to get rail journeys between Scotland and London down to three hours.
But Coalition sources last night suggested a vote for independence could throw any potential extension past Manchester into question.
A Downing Street source said: "If there is a Yes vote there are a lot of things we would have to look at. But at the moment Scotland is not 'on pause' as far as the UK Government is concerned."
The Scottish Government said HS2 must include Scotland to ensure the money spent on the project benefited Scottish communities.
Trains on the new line are expected to run to Birmingham from 2026.
The new study is the latest sign of ministers' commitment to the scheme, which is under scrutiny after Labour said it could pull its support if costs rose. Yesterday the Coalition admitted the economic benefits would be smaller than originally hoped.
A Scottish Government source said: "This is pathetic, petty scaremongering of the very worst kind which is only likely to backfire on Westminster by persuading more people in Scotland to vote Yes.
"The reality is that quality transport links are in everyone's interest and that will still be the case once Scotland is independent."