The Public and Commercial Services Union (PCS) has warned that it "cannot rule out industrial action in the face of such a serious attack" on its members' jobs, claiming the cuts will cause "carnage" in the public services.
Defending his plans, the chancellor told BBC Radio 4's Today programme: "The civil service unions should be in absolutely no doubt we are going ahead with these reductions, even if they threaten to strike.
"That would be a mistake, and counterproductive. We are going ahead with the reductions: they are both necessary and going to happen."
Mr Brown also rejected Conservatives claims that he will not be able to deliver his promised efficiency savings, saying mergers of back-room operations and use of new technology would make the cuts possible.
The shadow chancellor, Oliver Letwin, told Today: "If we want to get money on to the frontline of our public services, if we want to cut down on the flab in government, it's no good the chancellor saying that he is going to do more and more, and run more and more of people's lives.
"He has actually got to have a change of lifestyle. He's got to admit that the Government does not have to do so much. It must trust people more and interfere in people's lives far less."
Mr Brown said yesterday that his planned efficiency savings - and sale of £30bn of government assets - would help him increase spending on frontline services by more than 4% a year over the next three years.
With health and education budgets announced earlier this year, the chancellor said there would be more money for policing, security and defence and science and technology - all areas targeted by the Tories for savings as part of their pledge to cut public spending as a proportion of national income.
Mocking Mr Letwin, Mr Brown said the extra investment was "only possible because I have rejected the proposals of those who would cut spending on important services".
Some 20,000 more community officers would be recruited to back up the police with the extra money, while Sure Start children's centres would be rolled out to everyone who wanted them, he told MPs.
While Labour MPs welcomed the chancellor's spending plans, some were uneasy about his intention to unleash swingeing job cuts.
John McDonnell, chairman of the PCS Parliamentary Group, a cross-party group of MPs formed to strengthen the union's voice in Westminster, said 100,000 job cuts were "not to be taken lightly".
"Parliamentary colleagues have grave concerns for their own constituencies as these measures begin to impact upon local services and employment rates," he added.
His voice joins those of the PCS general secretary, Mark Serwotka; Jonathan Baume, general secretary of the civil service union, the First Division Association; and the TUC general secretary, Brendan Barber, who have all questioned the need for the cuts.
Threatening industrial action, Mr Serwotka said: "When this government was elected, they imposed the windfall tax to pay for initiatives like the New Deal; now they are using their own workforce to pay for their policies."
Mr Baume said the planned jobs cuts were "worse than we feared" and warned: "It's unlikely that this can be achieved without some compulsory redundancy."
Mr Barber, meanwhile, said: "These cuts cannot be made without hitting the quality of public services. They will deal civil service morale a bitter blow just as staff support is needed for change."
