Leaked proposals to axe 180 quangos have raised fears that thousands of jobs could be at risk.
The PCS union said they were a "disgraceful way to treat staff" and Unison have threatened industrial action if a school staff body is axed.
But some campaigners say job losses will be negligible and more quangos should be axed to save taxpayers money.
The Cabinet Office has ordered a leak inquiry and says it regrets any "uncertainty" for employees.
The list of public bodies up for abolition, merger or other reforms was included in a letter from Cabinet Office Minister Francis Maude to other ministers, dated 26 August, which was leaked to the BBC's Politics Show.
It includes the previously announced abolition of the Health Protection Agency, UK Film Council, Audit Commission and Human Fertilisation and Embryology Authority but also puts a question mark over the future of dozens of less well-known bodies.
The list suggests 180 quangos will be abolished and 124 merged. A further 338 will be retained, although 56 of them will be subject to "substantial reform". The future of another 100 bodies is yet to be agreed, according to the letter.
The Public and Commercial Services Union said thousands of jobs - and vital services - could be at risk.
General Secretary Mark Serwotka said: "This is a disgraceful way to treat staff who work hard and are committed to providing quality services, very often on low pay." He accused the government of being "happy to play politics with people's lives".
But Dan Lewis, of new think tank the Economic Policy Centre, said half of the quangos listed for abolition were just advisory bodies which "cost virtually nothing" to run: "What they are, are seven or eight people who meet in Whitehall five or six times a year and they pay the chairman £200 or £300 a time."
Conservative MP Douglas Carswell, who has campaigned for quango reform, told the BBC he wished more quangos were on the hit list, as they were spending public money irresponsibly.
"Far too many public policy decisions are made by quangos and the quango state when they ought to be made by those who are accountable to the public," he told BBC News.
Pressure group the Taxpayers' Alliance said there were "still lots more quangos that can be added to this growing bonfire".
But many of the unions representing quango staff have warned their abolition could harm public services and the economic recovery.
Construction workers' union Ucatt warned that privatising the Construction and Skills Training Board would be a "disaster" for apprenticeship training and the trade union Prospect said its members would be "very concerned for their jobs".
And Unison has threatened to ballot its members for industrial action over a proposal to abolish the School Support Staff Negotiating Body, which advises ministers on pay for school support staff.
Questions have also been raised about how much money would be saved. Crossbench peer Baroness Deech, a former head of the Human Fertilisation and Embryology Authority, which looks set to have its functions transferred to other regulators, told the BBC: "It only costs £5m and it's not taxpayers' money. Most of that £5m comes from the patients. Now if you redistribute the functions, you're not going to save anything."
Among quangos listed as facing abolition are the Advisory Committee on Organic Standards and Cycling England - whose functions will be transferred elsewhere.
The Olympic Park Legacy Company, responsible for planning what happens to the Olympic site after the 2012 Games, also faces abolition but its functions would be transferred. A spokeswoman said there had already been "significant progress" in discussions about it "evolving into a Mayoral Development Corporation".
'Not saving anything'
Postcom and Ofcom could be merged while the School Food Trust would have its status changed to an independent charity and Ofsted and the Food Standards Agency would be kept but subject to "substantial reform".
The future of the Student Loans Company, Visit England and Visit Britain, the UK Atomic Energy Agency, the Carbon Trust and the Environment Agency are yet to be decided, according to the document.
Last year Labour, the Conservatives and the Lib Dems all pledged to axe quangos with the aim of saving money.
The Daily Telegraph has published a similar, undated list of 177 quangos to be axed.
A spokeswoman for the Cabinet Office would not comment on the leaks but said the government had "made it clear that it is committed to radically increasing accountability and improving efficiency".
She added: "The cabinet secretary has this morning asked for an immediate investigation into the leak of a government document on Public Bodies reform. We deeply regret any extra uncertainty for employees that this irresponsible leak has caused".
Communities Secretary Eric Pickles told the BBC he did not know how accurate the list was.
He said: "We are certainly looking towards removing a number of unaccountable quangos and reducing their costs but we haven't come to a firm view with regard to the numbers. But we will be making an announcement reasonably soon."
Shadow Communities Secretary John Denham said the list appeared to show a lot of bodies facing abolition "actually have the job of holding the government to account... on behalf of the public".
He said: "If you've got a government coming along saying: 'Let's silence all the independent voices, let's silence the people who speak up about equalities ... they are really saying: 'We will be able to do whatever we like and there won't be anyone able to shine a spotlight on what we are up to'."