Newly independent senator Glenn Lazarus labelled it "blackmail".
"Australians should be angry that the Abbott Government is threatening to hurt people by cutting more jobs, including research and scientific positions, in order to try and blackmail the Senate into supporting deregulation," he said in a statement.
"This is disgusting behaviour and demonstrates the appalling ethics of this Government."
Another independent senator, Jacqui Lambie, who is in hospital, said she would "move heaven and earth to be in the chamber ... to vote against Pyne's vile legislation, even if it means being hooked up to a drip".
"Mr Pyne will need more than just a Kleenex I offered him at the start of this debate for the political pain I'm about to cause him," she said.
"He may need a dose of the intravenous antibiotic I've been on."
Another key crossbencher Nick Xenophon said scientific research cuts would turn Australia into a "dumb country" and send some of the nation's best scientists overseas.
"I just can't believe that Christopher Pyne is holding 1,700 scientists hostage to this policy," he said.
"This is not the way to negotiate with the Senate, it is reckless, it is irresponsible."
But Mr Pyne said he was confident of a breakthrough.-we'll see later this week.