More than two dozen research facilities are preparing to shut down as administrators warn Australian science is suffering “immense” damage as a result of the federal government’s refusal to guarantee critical infrastructure funding.

About $150m in funding for 27 research infrastructure facilities promised in last year’s federal budget has been tied to the Abbott government’s higher-education changes, which have stalled in the Senate.

The facilities have no guaranteed funding past 30 June and up to 1,700 jobs are at risk if they are forced to shut down.

Among the sites funded by the National Collaborative Research Infrastructure Scheme (NCRIS) is the Australian Microscopy and Microanalysis Research Facility, where scientists invented the Nanopatch, a needle-free vaccine delivery patch that could dramatically slow the spread of viruses during a pandemic.

Another NCRIS-funded site, the Australian National Fabrication Facility (ANFF), is developing a system to mass produce the revolutionary patch, but will have to shut its doors if funding isn’t renewed.

“We will close on the 30th June. There’s no magic bullet, there’s nothing up our sleeves,” ANFF chief executive, Rosie Hicks, said. “We are now entering the phase where we have to make wind-down plans.”

Even if the education minister, Christopher Pyne, relents and passes a bill funding NCRIS, the damage will already have been done, Hicks said. “Obviously we’re losing people. I’m being asked for references.”

Some of the facility’s 94 staff – all but three of them researchers or technicians – will take jobs overseas, and one has already left for Canada, she added.

The uncertainty also means the facility has not entered into any commercial contracts past the end of June, meaning revenue will likely fall even if the government money comes through.

Senate estimates heard last week the number of jobs funded in whole or part by NCRIS has grown to 1,700. Around 35,000 researchers use NCRIS facilities and services each year.

Fifteen heads of university and research institutions issued an open letter to Pyne on Thursday warning of the “immense” damage the closure of NCRIS facilities would do to Australian research, which they said would be “set back by several years”.

“[The] exodus of highly specialised skills has begun and will only accelerate as the end of the year draws closer,” the letter said. “Furthermore, many of the facilities cannot be viably maintained if taken offline for significant periods.

“This means that if operational funding for 2015-16 is not confirmed in the next two months, the government will be effectively decommissioning high-cost public infrastructure that in many cases has years if not decades of productive working life remaining.”

About $40m worth of data-gathering instruments could also be stranded in Australia’s oceans if the June deadline passes without renewal, Tim Moltmann, the director of the Integrated Marine Observing System (IMOS), said.

The agency, which deploys equipment to take scientific measurements in the ocean, has budgeted to run its instruments until June, “but no provision has been made for decommissioning”, Moltmann said.

He said its 80 employees were anxious about the June deadline. “Staff are nervous and some of our operators have already lost staff who didn’t necessarily want to leave but who have had to go and find more secure employment,” he said.

IMOS staff mostly worked regional hubs such Hobart and Townsville. “A majority of those positions are at risk without further funding,” he said.

An independent review of NCRIS due in May has reportedly found the program operates effectively and efficiently.

Hicks said the program was “world-leading” but that both major parties had only ever granted it short-term funding.

“We’ve been in a pretty difficult situation for a number of years with the funding being for quite short periods,” she said of her facility. “But we’ve never been three months from shutdown.”

Astronomer and Nobel laureate Brian Schmidt said the cuts would be a “hit to research like I have never seen in the 20 years I have been in Australia”.

“It really is the foundations of the research we do across the country, across all disciplines so it will have an enormous effect and it is something we cannot let happen,” he told ABC radio.

He said successive governments had invested more than $2b in the program over the past decade. “To suddenly put at risk the bridge between the past and the future such that all of that investment, $2bn over the last decade is suddenly put at risk, seems to be unconscionable,” he said.

“Ultimately, this is not the way a grown up country behaves. It’s very childish and it’s having a profound impact on something that is going to increase the productivity of the nation.”

Pyne said on Thursday it was Labor who set the funding deadline of 30 June, and that the government wanted to keep the program going. “That requires the [higher education] reform to pass to provide the savings,” he said in a statement.

“The funds for NCRIS only exist because of savings elsewhere in the higher education package.

“The way for Labor to support NCRIS, which they themselves defunded, is to support the higher education reforms.

“Labor needs to stop playing politics and enter negotiations with the government because it will be on the heads of Labor, the Greens and the crossbenchers if it closes,” he said.

Labor’s research and innovation spokesman, Kim Carr, said the government was holding the program “hostage” and could fund NCRIS at any time through an appropriations bill. “The reality is that the government is playing chicken with the country’s future,” he said.

The Greens science spokesman Adam Bandt said Pyne was “blackmailing the parliament, saying that unless the parliament passes his plan to increase university fees, he’ll take the axe to science and research facilities”.