The Shadow Chancellor insisted during a session at the TUC conference in Brighton yesterday that his party wanted to safeguard jobs ahead of pay rises for millions of staff.
He also reiterated Ed Miliband's message to the unions that the public did not want another wave of public sector strikes.
But he faced boos and heckles and calls of "shame".
Just hours later the conference voted to consider the practicalities of a general strike.
Mr Balls had been confronted by Liz Cameron, a 49-year-old youth worker from Manchester.
The mother-of-four wanted to know how Labour could support Tory-imposed pay freezes that she said left her wondering "whether or not I can pay my heating bills, whether or not I can choose to buy food."
She was cheered by delegates as she asked the Shadow Chancellor: "How on earth do you expect to get the support of hundreds of thousands of public service workers when you continue to repeat that position?"
But Mr Balls insisted pay restraint was needed to help save jobs. He said at a time when hundreds of thousands of public sector workers were facing the sack, his party could not argue for anything that would make their situation more precarious.
He told the youth worker he was "not doubting" the difficulty of her situation.
But he said: "The fact is over the next three to four years the Government is planning radical budget cuts which will lead to the loss of 700,000 jobs in the public sector.
"In order to avoid wholesale compulsory redundancies, people are saying we are going to continue with pay restraint and jobs have got to come first."
But there were jeers from the crowd as he added: "We always, as a movement, have said jobs first. It is the right argument for us. I want things to be done in a fairer way but I don't think we can argue pay before jobs. We have got to say jobs before pay."
He also echoed Mr Miliband's message to trade union leaders when he addressed them at a dinner in Brighton on Monday night, that the public "does not want strikes".
Last night Dave Prentis, general secretary of Unison, said that if Mr Balls really understood the impact of three years of falling wages on struggling families "he too would be calling for an end to the pay freeze."
Meanwhile, public sector unions in Scotland have warned John Swinney his proposed "modest" pay rise next year will be unacceptable to workers if it is simply the same 1% on offer from the UK Government.
The Scottish Finance Secretary fuelled optimism this week by saying he aimed to honour his commitment to bring in modest public sector pay increases in 2013-14.
He said: "I promised the public sector workers of Scotland 12 months ago that I hoped we would see the beginnings of the end of the public sector pay freeze, and I am going to work to try to deliver that."
But while these comments appear to raise the prospect of a more generous settlement for public sector staff north of the Border, the unions are sceptical.
Grahame Smith, general secretary of the Scottish TUC, said: "If his 'modest' is a fraction of a percentage, then I don't think that's acceptable given that there is a necessity to deal with pay increases that are contractually obliged. He certainly has some flexibility to do something around pay, although he is restricted on one hand by the settlement from the UK Government and some of the commitments he's already made.
"Some of them, including the council tax freeze and the small business bonus, are not justified or sustainable."
Dave Watson, Scottish organiser of Unison, said: "He did use the phrase modest, and I suppose 1% does come into that category. The truth is that the Scottish Government position has mirrored the UK position on public sector pay at every stage."
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