Public servants at the Fair Work Ombudsman could be paid bonuses worth hundreds of dollars if they can improve their record for showing up to work.

A Senate Estimates Committee was told on Tuesday morning that a one-off bonus of .25 per cent of annual wages was on the table in the agency's bargaining talks, conditional on a reduction in the rates of "unscheduled absence" at its workplaces.

The payment would be worth $225 to a public servant earning the agency's average annual salary of $90,000.

The Ombudsman's public servants clocked up an average of 2½ weeks in sick leave and more than three weeks of unscheduled absence in 2013-14, more than three days above the Australian Public Service median rate.

The agency's sickie problem is getting worse, with no-shows among its 790 workers increasing by more than 20 per cent from the previous year.

Deputy Ombudsman Michael Campbell told the committee that he and his colleagues were keen to bring down the rate of absenteeism at the agency.

Under questioning from Labor senator Sue Lines, Mr Campbell said the one-off bonus might be part of an enterprise bargaining deal that would also include a 3.25 per cent wage rise over three years.

"We will negotiate the terms and the way it works but the intention is that if we can decrease our unscheduled leave absence globally, right now we're talking about two days, then we would provide a one-off bonus of a quarter of a per cent," Mr Campbell said.

"But the features of that would be negotiable."

"It's also a productivity benefit."

Senator Lines wanted to know if the agency was trying to get sick workers to show up to the office.

"We're not trying to encourage a sick workforce, Senator, what we're trying to do is deal with instances were unscheduled leave could be avoided," Mr Campbell replied.

"It's also about making the workplace a workplace that people want to come to, so there's a whole range of issues.

"The intention behind positive attendance culture is having an open and honest conversation about what might be going on and helping staff manage it better."

The committee also heard from Departmental of Employment Deputy Secretary Sandra Parker, who said that bosses across the public service were struggling to control rising levels of absenteeism, but there were still no clear answers about what was causing the problem.

"It's difficult to say, it goes in parallel  to the rise in mental stress claims through workers' compensation," Ms Parker said.

"It doesn't overlap entirely, but there's often evidence that when someone is staying away from work regularly it may lead to them getting an injury or a stress claim.

"If there is an issue with their supervisor or an issue in the workplace … it can obviously lead to them going to a doctor and at some point putting in a workers' compensation claim for mental stress."

Ms Parker outlined a non-punitive approach to workplace absences that aimed to deal with problems before they escalated.

"What we want to do is change the conversation so that the approach is not about 'where are you and why aren't you at work', the approach is 'can we help you, is there something you need to talk about with us, is there a problem with your workplace, your supervisor'," the deputy secretary said.

"So [it is] trying to get ahead of it rather than getting to a point where the person is so sick they're never coming back to work."