The current process lacks transparency and independence from government, says the Australian Defence Force Welfare Association, which led the backlash by the military rank and file that forced two backdowns by the Abbott government over pay and conditions in recent months.

In its submission to the latest ADF wage determination, made public on Wednesday, the association argues the pay debacle, which lasted seven months and forced two embarrassing political reversals by the government, would not have happened under a more open and transparent system.

The government was forced to reverse its position twice after sailors, soldiers and Air Force personnel mounted a grassroots campaign against moves to cut conditions and entitlements for a pay rise of 1.5 per cent a year.

The eventual position was locked in on Tuesday by the Defence Force Remunerations Tribunal, which also confirmed that the pay rises would not be backdated, meaning ADF personnel will miss out on $25 million in wages.

The present system sees the government instructing the Chief of the Defence Force on the wage determination for the Navy, Army and Air Force with the decision effectively rubber-stamped by the Military Remuneration Tribunal.

The ADF members do not vote to accept or reject a proposal and cannot take industrial action if they have a grievance.

In its submission to the tribunal the welfare association argued for reform of the whole system.

"The repeated intervention of the government to improve the pay offer to ADF personnel highlights the inadequacy of the original offer and also the unfairness of the process followed to determine ADF salary adjustments," association executive director Alf Jaugietis said.

"Even the tribunal started to doubt the fairness of the process under which it had to work and that its hands were tied to make a decision outside of the agreed positions."

In its final determination, published on Tuesday, the tribunal remarked that the backlash by Australia's rank-and-file military personnel against the Abbott government over wages was entirely predictable.

The official body was scathing on how the process was handled.

The two government backdowns came after a spirited campaign led by the Australian Defence Force Welfare Association, which mobilised an online backlash from the families of ADF members, with the military personnel themselves barred from taking industrial action.

With crossbench politicians and veterans' groups later joining the campaign, Prime Minister Tony Abbott was forced to intervene to limit the political damage the row was doing, and increased the wage deal to 2 per cent a year.

The three-person tribunal wrote on Tuesday that it was quite predictable that the initial proposal, which was well below inflation forecasts at the time, would foment trouble in the ranks.

"In our opinion, prior to the workplace remuneration arrangement first being agreed, it was known or could reasonably have been expected that there would be dissatisfaction with the quantum of the increase," the tribunal wrote.

"Although we accept the CPI has not traditionally been determinative of the quantum of increase [nor should it be], nonetheless it could not have been a surprise that the below CPI quantum of pay increase in the WRA would be criticised."