A successful bid for the so-called European Spallation Source (ESS), which would be the world's largest neutron scattering research facility, has for years been considered the region's top economic development project.
The scheme has been compared t
o the Olympics for its potential to generate jobs and wealth.
Regional development agency Yorkshire Forward, Leeds, Sheffield and York universities and the Leeds City Region collaboration of 10 local districts have spent vast amounts of time, effort and money on the drawn-out bidding process.
But it emerged last night that Yorkshire Science, the region's science and innovation council, received a letter "out of the blue" saying the Government had taken a "strategic decision" to only support proposals for major new facilities in the established science campuses at Daresbury in Cheshire and Harwell in Oxfordshire.
The letter, to Yorkshire Science chairman Richard Gregory, was dispatched by Lord Sainsbury just two days before he resigned last week as Science Minister.
Blueprints have suggested that the facility – on 540 acres at the former Burn airfield, near Selby – would employ up to 2,000 people in construction and 1,000 more to run it for 50 years.
Selby MP John Grogan hit out last night at the letter, saying it appeared to not only rule out the ESS project but any future strategic science investment in the region.
"Without doubt Lord Sainsbury was trying to kill off Yorkshire's bid to host a major science facility as he was clearing his desk," he said.
"The truth is that he has always favoured the Oxford scientific establishment and in the meetings I have had with him he has always seemed rather disdainful of the merits of the north of England and the world-class science to be found here.
"The ESS project is potentially as important an economic driver to Yorkshire as the Olympics will be for London. We cannot let Lord Sainsbury's letter stand as official Government policy."
Mr Grogan said he would be taking up the offer of a meeting with new Science Minister Malcolm Wicks.
He added: "As a former lecturer at York University, I hope the new Science Minister will take a more enlightened view of the scientific and economic potential of Yorkshire."
Yorkshire Forward chief executive Tom Riordan also expressed dismay last night at the letter.
"This is a big surprise to us. We need to know if this was just Lord Sainsbury's thinking or whether it really is the consensus across Government," he said.