Mr Balls replied that in the current economic climate, jobs were more important than pay rises.
"When you are losing hundreds of thousands of jobs, you cannot say the first priority is more pay for public sector workers. That is the reality because of the Government's failure on the economy. We have always said let us put jobs first."
He was booed and heckled by delegates over his comments, which later drew criticism from union leaders.
Dave Prentis, general secretary of Unison, said: "If he really understood the massive impact of a three-year pay freeze on families struggling to pay for food and fuel, or forced to turn to pay-day loans where interest can be a terrifying 4,000%, he too would be calling for an end to the pay freeze."
Bob Crow, leader of the Rail, Maritime and Transport union, said: "It's all very well Ed Balls wading into the Government but what working people want to know is when the Labour front bench is going to stand side by side with us on the picket lines and out on the streets."