Ed Balls has accused the government of "itching" for a confrontation over public sector pay, but has been heckled by trade union members for refusing to back the repeal of a multi-year wage freeze.

The shadow chancellor told delegates at the annual Trades Union Congress in Brighton that strikes must be a last resort, after the conference backed a motion calling for co-ordinated walkouts over pay. The TUC is also expected to back a motion to explore the "practicalities" of staging a general strike.

Echoing comments by Ed Miliband at a TUC dinner on Monday night, Balls told delegates that walkouts would be unpopular with the rank and file as well as the public. "I am sure that the last thing the vast majority of trade union members want, at a time of such uncertainty, is strikes over the coming months. It is not what we want. It is not what the public wants either," he said.

However, to applause, he added: "But when coalition ministers warn that they will have to act and legislate if we see a return to the unrest of the 1980s, what we are really seeing is Tories itching to provoke a row about strikes so they can blame the stalling recovery on trade union members and working people."

Balls and Miliband drew sharp rebukes this year from the three largest unions – Unison, Unite and the GMB – for backing a public sector pay freeze that will continue in 2013/2014 and 2014/2015 with a 1% cap on raises.

The shadow chancellor faced sustained heckling during a question and answer session after his speech, when he refused to back down on his support for pay restraint. Balls blames George Osborne's failure to generate a sustained economic recovery, which he says has left Labour's hands tied on pay.

Liz Cameron, 49, a local government worker, said to resounding applause from the floor: "Why is it that when we look to Labour to support us, we hear you and Ed Miliband supporting this Tory pay freeze? How will you win the support of hundreds of thousands of public sector workers when you continue to repeat this policy?"

She described herself as a "proud public service worker" in the third year of a pay freeze, the impact of which has been exacerbated by a 12% increase in inflation over that period. She told Balls that low-paid workers were having to save money on food and cut back on buying new school uniforms.

"Times are tough and so many of us are really struggling – care workers, teaching assistants and dinner ladies – fighting to make ends meet. Saving money on food, no new school uniform for our kids, cutting back on heating costs," she said.

Balls, who was shouted at from the floor when he refused to reverse some coalition tax rises and spending cuts, told Cameron that "you have to put jobs before pay", as he argued that wage increases would be paid for with job cuts. "Jobs have to come first and I think that is the right choice at the moment," he said.

"We cannot say that the first priority is more pay for existing workers when hundreds of thousands of workers are losing their jobs," he added, referring to estimates that 700,000 state-backed jobs will go by 2015.

Balls's response was criticised in a followup question from Janice Godrich, national president of the Public and Commercial Services union. She said: "I found your answer to public sector pay extremely disappointing. I would like to see the Labour party standing up for public services and standing up for public sector workers."

After the session, the national secretary for public services at the GMB, Brian Strutton, said: "I understand the need for him to be extremely cautious. But I think he could find a way of expressing that message and doing it in a way that does not upset the audience he is speaking to."

Balls also refused to back a question from the RMT union, greeted with loud cheers, calling for the nationalisation of the rail industry, amid a row over the future of the west coast rail franchise. The shadow chancellor said such a move would cost "billions of pounds", and a Labour government would concentrate on making existing franchise contracts work more efficiently.