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Martha Crago is the vice-president of research for Dalhousie University. (CBC)

Nova Scotia's universities are speaking out for the first time about federal government research cuts now emerging from the recent budget.

"This came as a surprise to the research community and a very unwelcome surprise," said Martha Crago, the vice-president of research for Dalhousie University.

"This is like trying to imagine having to prepare meals in your home without a stove."

Crago said Dalhousie University received $1 million for equipment last year through the federal government's Research Tools and Instruments grants program. The program is being eliminated next year to save money.

Another equipment granting program called Major Resources Support is under a moratorium.

"When somebody has to cut something, they have to figure out where they cut it from. And this is the particular choice that was made," Crago told CBC News.

Both programs are funded through the Natural Sciences and Engineering Research Council of Canada. The money is used to replenish research technology and is considered by researchers to be fundamental to basic science.

"It has important implications both for the science that can be done in Canada and for the retention and attraction of people to come work in Canada," said Crago.

"This has been a useful program to natural science researchers and for the training of highly qualified people.

It's unclear clear what, if anything, will replace the existing grant programs.

Kevin Vessey, the associate vice-president of research at Saint Mary's University in Halifax, said that concerns him.

"There is no alternate so that's the great quandary in my mind. Where do we go?" he said Thursday.

Too many programs, says minister

Vessey credits a $65,000-grant from Research Tools and Instruments for the purchase of an environmentally controlled cabinet that is critical to his research into biofuels. The research that followed was decisive in helping Vessey establish a research lab at Saint Mary's University in 2005.

He acknowledged the importance of industry-partnered university research, but said younger scientists will pay the price.

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University researchers say younger scientists will pay the price with federal budget cuts. (CBC)

"We've invested a huge amount of money in these people in terms of their graduate programs, their training," said Vessey.

"Then we put them in a laboratory but don't give them the tools to actually do what they were trained to do. That's a real problem."

At the Canada-Wide Science Fair in Charlottetown on Thursday, Minister of State for Science and Technology Gary Goodyear said federal research spending is at record levels, but there are too many programs.

"We need to improve the efficiencies," Goodyear told reporters.

"How many programs are out there that do the same thing and how do we combine them to make sure that the accessibility stays the same, the amount of funding stays the same but scientists are looking at two or three programs instead of 36?"

Nova Scotia's universities say one option under consideration is to ask researchers apply to the Canadian Foundation for Innovation for equipment purchases.

That program is jointly funded by provincial governments and would tie funding to the ability of provinces to match federal spending.

"That may lead to regional disparities across the country depending on the wealth of various provinces to meet these matches," said Crago.

"It's something I worry abut for Nova Scotia and Atlantic Canada, frankly."

A spokesperson for the Nova Scotia government said the province is monitoring the situation.