According to recently revealed figures, HS2 would make 50 areas across the UK worse off, with Aberdeen being the worst hit, followed by Norfolk East, and Dundee and Angus.
These figures were omitted from the Government-commissioned report on the high-speed English rail link when it was published in September.
Scotland's Transport Minister, Keith Brown, said: "This information reinforces the case that the Scottish Government, business and civic Scotland have been making, which is that HS2 must include Scotland in order to realise economic benefits for our communities.
"It also amplifies the point that the business case for the project is strengthened if Scotland is included."
UK Transport Secretary Patrick McLoughlin defended the controversial project, insisting he had "no doubt" that the scheme would benefit the UK as a whole.
The comments came after previously unreleased research listed more than 50 areas that are likely to end up worse off.
In September, ministers hailed a KPMG report that concluded HS2 would boost the British economy by £15 billion a year.
But while it listed the areas that would benefit, such as Greater London by £2.8 billion and the West Midlands by £1.5bn, it omitted details of those that would end up worse off.
The full findings were released in response to a Freedom of Information request.
Among those hardest hit would be Aberdeen, losing £220m, Cambridge, which would lose £127m, Bristol with £101m, and Essex South with £151m.
McLouglin said: "All these investments that we are looking at is to serve the people of the UK, [and] to make the UK a place where we attract investment. It's of no doubt to me that it's beneficial to the UK."
He said the report showed that HS2, which would connect London to Birmingham, Manchester and Leeds, would give a £15bn boost to UK plc.
"HS2 is vitally important overall for the long-term future of the economy," he added.
Professor Henry Overman from the London School of Economics - formerly an expert adviser to HS2 Ltd - said it was obvious that, as some cities, towns and regions reap the benefits of being better connected, other places away from the line will pay a price.
"When a firm is thinking of where to locate, it thinks about the relative productivity of different places, and the relative wages," he said. "HS2 shifts that around."
The chief executive of HS2 Ltd, Alison Munro, said: "What this is showing is that the places that are on the high-speed network ... are the places that will benefit most from high-speed two.
"But high-speed two isn't the only investment that the Government is making. Over the next five years it is planning to spend £73bn on transport infrastructure."
A Department for Transport spokesman said: "These figures show that the new north-south railway is vital to rebalance our economy and it boosts the north overall more than the south. Of course, the line does not serve every city and region and these figures reflect that. But it is wrong to take them in isolation. HS2 is part of a much bigger boost to our transport system: £73bn in the next parliament, of which HS2 is just £17bn. This will massively benefit places HS2 will not serve long before the line opens."
Jonathan Isaby, political director of the TaxPayers' Alliance, said: "It's utterly dishonest for the Government to have spent £250,000 of taxpayers' money on a report and then to release only cherry-picked findings.
"This is further evidence, if it were needed, that the KPMG report was a taxpayer-funded propaganda exercise. Sadly, HS2 bosses have a track record of using dodgy numbers in an attempt to justify the white elephant's hefty price tag. It's time to scrap this project before any more taxpayers' money is wasted on its construction or its expensive PR."
David Bell, professor of economics at Stirling University, explained that the figures were based on the potential loss of business the cities could face if the rail link goes ahead as the financial dividend of the development would be centred around the south of England and the Midlands.
Bell said £220m could equate to roughly 1000 potential jobs that would not be created if business decided to go elsewhere.
He argued that if "economic activity" was "concentrated towards the new HS2 line" that would "draw commerce away" from areas like Aberdeen.
He added: "An example might be a factory that has the option of being sited in Aberdeen or Birmingham - it now tilts the balance in favour of Birmingham."