A study examining the potential of running 250mph trains to the north of England and Scotland will be completed early in 2013, though Scottish Government officials said they were unaware of it.
The announcement follows a torrid week at the Department for Transport, which was forced to abandon the award of a £13 billion contract to run West Coast passenger trains between Scotland and London to First Group last Wednesday following a legal challenge by Virgin Trains.
First, which had £244 million wiped off its share value, is considering whether to sue the UK Government.
A spokesman for the Aberdeen-based company said it was still awaiting a briefing from the DfT on who would take over the West Coast route on December 9, when Virgin's existing contract expires.
The Coalition has endured fierce criticism, including from Conservative backbenchers, over its commitment to building a £33bn route connecting London to Birmingham by 2026 and extending it along separate branch lines to Manchester and Leeds by 2033.
Mr McLoughlin said: "We can't afford not to build it. Our competitors around the world are investing in the best transport, and we must too."
On extending the line north of Manchester and Leeds, he added: "We're launching a study on the way to get fast journeys further north still, with the aim of getting the journey from Scotland to London to under three hours and making sure the North East benefits too, because this will be a scheme for every person in Britain."
A DfT spokesman said the study would look at "capacity and journey times" and involve Government agency Transport Scotland.
However, the agency said officials had no knowledge of the study.