Employees were offered a single, upfront increase: a 2.6 per cent raise for a three-year agreement, which equates to about 0.86 per cent a year. If the year-long delay in bargaining is taken into account, the pay rise is worth about 0.64 per cent a year.

The workplace's main union had recommended rejecting the deal, saying it cut conditions and real wages.

Comsuper, which has about 450 staff, will cease to exist in two weeks when it joins the Commonwealth Superannuation Corporation, though the new enterprise agreement will remain in effect for employees who transfer across.

The ballot was held on Friday and about two-thirds of the staff who voted accepted the proposal. They had rejected an earlier offer.

Earlier this month, taxpayer-owned business NBN Co became the first federal government employer to strike a wage deal with its staff under the Coalition's tough bargaining rules.

Enterprise agreements covering about 150,000 public servants expired almost a year ago and, until this month, no agency had successfully negotiated a new deal for its workforce.

Under the government's bargaining policy, employers must fund any proposed pay rises through administrative savings or by "cashing out" staff benefits.

Comsuper funded its pay rise by abolishing some executive-level jobs, limiting higher duties allowance to staff who are in senior roles for at least 10 days, tightening the requirements for performance-based pay increases, and reducing staff hours away from work by improving the agency's "timekeeping" system.

Public Service Commissioner John Lloyd welcomed the outcome, commending Comsuper's staff and executives.

"The agreement was strongly supported by staff despite significant opposition from the union, including an attempt by the [Community and Public Sector Union] to delay the process in the Fair Work Commission," Mr Lloyd said.

"This result, along with the three enterprise agreements recently voted up at NBN Co, shows what can be achieved when employers and employees work together for a mutually beneficial outcome."

The union had advised staff last month to vote "no", saying the offer was worse than those in other public service workplaces.

"Remember, Treasury have made an offer of 4.5 per cent ... over three years. By voting no [previously], Comsuper staff have already secured a better deal. By voting no again, if necessary, staff can secure a decent deal that doesn't leave you short-changed," the union said.

A Comsuper spokeswoman said on Tuesday the agency believed its proposal won support because it "offered staff certainty and stability and provided a pay rise with minimal change to key employment conditions, which are important to many staff".