Salaries of public service bosses will grow by up to $17,500 in a round of pay hikes coinciding with warnings of continuing sluggish national wage growth.

Pay packets for departmental secretaries and other agency heads are set to rise 2 per cent on July 1 in a Remuneration Tribunal decision released on Wednesday, coming after most bosses ended long-running industrial disputes over wages and conditions with their staff.

The pay rise for top Australian Public Service staff will bring the salary of Prime Minister's department boss Martin Parkinson to about $896,400 on July, up from $878,900.

Treasury secretary John Fraser's annual salary will top $874,000, and Defence Department secretary Greg Moriarty, Finance boss Rosemary Huxtable, Home Affairs' Michael Pezzullo, and Human Services Department top public servant Renee Leon will see their salaries grow.

The outgoing public service commissioner John Lloyd, and his successor after he finishes in August, will receive $706,000 a year, rising from about $692,000, following the pay rise.

Reserve Bank governor Philip Lowe's warning of possible continued slow wage growth, a positive economic outlook in federal budget papers and the government's decision to keep capping public servant pay rises in its new workplace bargaining policy were behind the tribunal's decision.

Wage rises in state and territory public sectors had also been restrained, between 1.5 per cent to 2.5 per cent, the tribunal said.

The latest pay rise for APS bosses follows another 2 per cent increase last year, which was one of only three since 2013 as the Remuneration Tribunal responded to low wage growth and an "environment of economic restraint" by increasing salaries less often and at lower rates.

National wage growth has fallen below market expectations as workers' pay increased by just 2.1 per cent in the year to March, and recorded its second-weakest quarterly result in two decades.

The Home Affairs Department, the Bureau of Meteorology and the Australian Institute of Aboriginal and Torres Strait Islander Studies are among the last federal agencies to reach a workplace deal following years of bitter industrial disputes.

Many public servants went several years without pay rises in the last round of bargaining.

The prolonged workplace battles failed to soften the Coalition government's new bargaining rules for public servants released in February, keeping a cap on pay growth and continuing policies blamed for the industrial strife.

A 2 per cent ceiling on yearly wage rises for public servants since 2015 has capped rank-and-file pay growth ahead of predicted inflation, while the public service commission's previous workplace policy was singled out by critics as a major cause of the bitter industrial impasses.

Under the new policy covering the next round of bargaining, the government has maintained its wage growth cap.