The public sector union has accused the Federal Government of deliberately dragging out pay negotiations with more than 100,000 public servants in a bid to save hundreds of millions of dollars.

The figures, provided by the Australian Public Service Commission (APSC), reflect the estimated financial cost to public servants after multiple departments rejected offers during a tumultuous enterprise bargaining process spanning several years.

The departments of Human Services, Defence, Agriculture, Immigration and Border Protection and the Australian Tax Office — the five largest agencies — were among those left without an agreement.

The APSC figures reveal wages foregone or deferred by workers at those agencies amounted to $343 million.

The Department of Human Services topped the list, with workers losing about $114 million in pay rises, followed by the Australian Tax Office at $85 million and Defence with $69 million.

For an individual employee working for the Bureau of Meteorology, it resulted in an estimated $3,873 in foregone wages for an APS 5 level or $5,805 for an executive level 1 (EL1).

The figures were provided by the APSC in response to a question from Senator Bridget McKenzie at budget estimates late last year.

Community and Public Sector Union (CPSU) assistant national secretary Michael Tull said "it was always the Federal Government's intention" to delay an agreement and save itself money.

"It is very disingenuousness for the Government to be claiming that it's somehow the union's fault that people didn't get these pay rises," he said.

"In fact, it was the Government's deliberate strategy to apply a form of industrial blackmail to this round of bargaining.

"They proceeded to try to spin their way out of trouble."

'The Government doesn't achieve savings through delays'

But in its response to Senator McKenzie, the APSC said agencies must meet the cost of any wage increases within their existing budgets and the $343 million could not be considered a saving.

Australian Public Service Commissioner John Lloyd said the implication that the Government intentionally protracted bargaining was "flawed".

"Government does not achieve savings through delaying new enterprise agreements," he said.

"Agencies don't receive budget supplementation to pay for wage increases.

"The real losers are the employees. The CPSU strategy meant that they received pay increases much later than they should have."

The figure of $343 million covers several years of pay negotiations, as staff rejected offers — and sometimes went on strike — over what the CPSU termed "draconian" cuts to conditions and workplace rights.

"The Government's plan quite clearly was … to starve people out with a pay increase in the hope that eventually those workers would just give in under cost of living pressures and sign agreements that would do away with important workplace rights and conditions that they'd built up over the years," Mr Tull said.