The government has been accused of attempting to suppress the drawbacks of its flagship transport project after previously unseen research revealed cities across the UK could lose up to £220m each as a result of HS2.

The KPMG study, commissioned by the government, predicted more than 50 areas would be worse off as a result of the high-speed rail project – including Bristol, Cambridge and Aberdeen.

However, these findings were omitted from the report published by the government in September, the BBC reported, and only released after a freedom of information request by the BBC's Newsnight programme.

In September the Department for Transport hailed the study – which found the UK economy would be boosted by £15bn a year – and listed the areas that would benefit, including Greater London (£2.8bn) and the West Midlands (£1.5bn).

But the areas that would lose out have now been revealed, with those worst affected by a drop in economic output including Aberdeen (£220m), Cambridge (£127m), Bristol (£101m), and southern Essex (£151m).

The accountants used data from HS2 Ltd's assessment of the direct transport impacts of the scheme, which would connect London to Birmingham and to Manchester and Leeds.

Professor Henry Overman from the London School of Economics – formerly an expert adviser to HS2 Ltd – told the BBC it was obvious that, as some cities, towns and regions reap the benefits of being better connected, other places away from the line would 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 etc," he said. "HS2 shifts that around."

The chief executive of HS2 Ltd, Alison Munro, told Newsnight the figures were unsurprising. "What this is showing is that the places that are on the high-speed network … those are the places that will benefit most from high-speed two.

"But HS2 isn't the only investment that the government is making. Over the next five years it is planning to spend £73bn on transport infrastructure."

Anti-HS2 campaigners accused the government of having "deliberately suppressed any findings that would make HS2 seem bad".

The campaign manager of Stop HS2, Joe Rukin, said: "We have always said that London would be the biggest winner from HS2 and the hidden part of this report backs this up. We have always said that HS2 would suck economic activity away from places which cannot afford to lose it and the hidden part of this report backs that up too."

The former transport minister Lord Adonis, who was responsible for the HS2 project during his time in government, said it was a vital "national grid, connecting up the economic heart of the country".

He said that to not go ahead with the rail link would be tantamount to "closing Britain for business", adding that "no other country with our economics or geography has taken this ridiculous [anti-HS2] attitude".