Unions say they will not be silenced or intimidated by the Queensland Government's attempt to take them to court over doctors' contracts.

Queensland Health has applied to the Federal Court in Brisbane in a bid to stop information "misrepresenting" the Government's position on individual employment contracts.

Unions have said doctors could lose a third of their wages under the new contracts and they would also lose protection from being sacked.

Queensland Health director-general Ian Maynard says the unions are exaggerating and not being factual and that is why legal action is being taken.

"These proceedings do not injunct unions and professional organisations from talking with their doctors and presenting information," he said.

"I openly encourage unions and professional organisations to talk with our doctors.

"This application targets specific documents which are dressed up as legal opinion and they are not legal opinion."

But Together Union secretary Alex Scott says the move will escalate the dispute and the Newman Government's answer to everything is legal action.

Sorry, this video has expired Health Minister says doctors don't need to quit ( Matt Wordsworth )

"This would have cost the Government tens of thousands of dollars in taxpayers' dollars for an interstate law firm to come up with a novel and completely illegitimate legal basis for law that is not relevant for Queensland and not relevant for the doctors dispute," he said.

"Once again we are seeing taxpayers money flushed down the toilet to try and silence the criticism of this Government."

Mr Scott says it is a bullying tactic.

"I think we are seeing a new low in desperation from this Government because they're not only attacking (corruption fighter) Tony Fitzgerald and (former solicitor-general) Walter Sofronoff and the whole legal community, they are now taking action through the courts to try to stop what is a very significant debate about the future of the hospital system," he said.