The government rolled seven commissioner positions into four in its new Human Rights Commission, which came into being in April.

The seven separate commissioners were all (except one) on substantial pay packets of $196,100. Three of the new commissioners will be paid $188,600 from July 1. The other position, of president, will be paid $216,100.

The government had asked for a downgrade of the jobs other than president to executive level 1.3, which would have meant a salary of $176,600.

But the Remuneration Tribunal rejected the request, opting instead for a pay-rate halfway between level 1.3 and the next level, 2.4.

Tribunal chairwoman Anne Cahill Lambert confirmed the decision on Sunday, saying while it was understandable that a government agency would want to save money "we just thought that the work they do was still too important to leave down at that very low level".

"While there is going to be a clear leadership role [for the new president], nevertheless the work the other commissioners do is still incredibly important," she said. "They might have to, for example, criticise government, and that is a serious matter."

The government has rolled the jobs of children's commissioner and public advocate into one job. It has also combined the jobs of disability, discrimination and health service commissioners into one. The Victims of Crime Commissioner remains a separate job, with the salary increased from $142,900 to $188,600, bringing it in line with the other commissioners.

In a submission to Ms Cahill Lambert, the government's deputy director-general of justice, Vicki Parker, asked for the pay reductions to executive level 1.3, saying it reflected the responsibilities of the new positions.

Overall leadership, responsibility and strategic planning would now be in the hands of the president, who would also be the public face of the commission and senior to the other commissioners, justifying a pay rise for that position. Individual commissioners would no longer have to manage their own budgets or staff, but would focus on service delivery, Ms Parker said.

The changes were not decreasing the value of the Human Rights Commission, but were necessary to "future proof" the agency "in a tight budgetary environment", she said.

Ms Cahill Lambert also questioned the disappearance of a separate domestic violence coordinator from the full-time statutory positions. In her reply, Ms Parker said she had been made coordinator-general for domestic and family violence. Given her appointment, the role of the domestic violence coordinator in the former structure "is not clear at this time", she said.

In other decisions released on Friday, the tribunal awarded big pay increases to the head and deputy of the ACT Legal Aid Commission.

Chief executive John Boersig receives a whopping $50,400 pay rise on July 1, up 24 per cent, to $261,200. His deputy receives a 17 per cent pay rise, to $200,100.

Mr Boersig's new pay-rate puts him on a par with the head of the ACT government's Land Development Agency, but still $30,000 behind the auditor-general and the head of the Canberra Institute of Technology.

In its decision, the tribunal said the big increases for the two top bureaucrats in the Legal Aid Commission recognised the changes in the scope of their work since 2003 and the "increases in work value attached to the two jobs". It had made the change after a submission from Legal Aid, which the agency had requested remain confidential because it included information on comparable salaries in other states.

The Remuneration Tribunal gave most full-time statutory office holders a 2.5 per cent pay increase from July, in line with the amount it awarded to the 231 executive-level public servants, but less than the 4 per cent pay rise that goes to politicians.