The acting boss of a federal Parliament House department recently raided by the National Anti-Corruption Commission (NACC) has been unable to tell Senate estimates when the secretary will return to work.

The Department of Parliamentary Services (DPS), which oversees the Parliament House, has been rocked with accusations this year, including of harbouring a toxic culture, the silencing of dissent and the routine cover-up of problems. 

It has also been subject to revelations about a relationship between the department's boss, Rob Stefanic, and deputy, Cate Saunders, which led to Ms Saunders leaving the public service with a more than $315,000 payment. 

Mr Stefanic has been absent from DPS for almost a month and senators had requested he appear at Senate estimates to face further questions on Monday.

But acting secretary Jaala Hinchcliffe said Mr Stefanic was on paid leave, with no end date, and would not be able to attend the hearing. She refused to outline the nature of his leave. 

In a wide-ranging appearance, Ms Hinchcliffe confirmed she was notified about the raid on DPS the day before NACC officers executed a warrant to search the department at Parliament House on October 3. 

She also told estimates that she had commissioned barrister Fiona Roughley SC to conduct an "independent fact-finding investigation into the department's role in the incentive to retire payment" that Ms Saunders received. 

At estimates earlier this year, Mr Stefanic insisted he was not in a relationship with Ms Saunders when she was his deputy. He disclosed a verbal conflict of interest with the public service watchdog because of "perceptions of a close relationship" with Ms Saunders.  

The verbal declaration occurred eight months before Ms Saunders went on a secondment to Services Australia. Two months after the secondment started, Mr Stefanic verbally disclosed a "personal relationship" with Ms Saunders to parliament's presiding officers — House Speaker Milton Dick and Senate President Sue Lines.

Estimates is one of the rare moments of transparency for DPS because, as the ABC revealed earlier this year, a temporary change made more than a decade ago made the department exempt from freedom of information requests. 

At Monday's hearing, Liberal frontbencher Jane Hume wanted to know why Mr Stefanic had not made the conflict of interest declarations in writing, as a DPS policy outlines. 

Ms Hinchcliffe said she was unable to say why it wasn't in writing.  

Senator Hume alleged the presiding officers "potentially have been misled" over the nature of Mr Stefanic's conflict of interest declarations. 

"So we've got no record of the declarations of this conflict, we've only got recollections," she said.

"We've got inconsistent stories about who knew what and when, we've got an inconsistent and at best patchy record of when the department was told about a secondment for the deputy secretary.

"And in fact, it may have had more of a role in arranging it than anyone was aware but we won't know because it appears that nothing has been written down. We have had to take a lot of this on trust because the department is not subject to freedom of information."

Ms Hinchcliffe said throughout her career she had observed the public service had issues with record keeping.

She said addressing that would be a priority during her leadership of the department. 

Ms Hinchcliffe was an interim commissioner at the NACC prior to working at DPS. 

Senator Hume said she was pleased Ms Hinchcliffe had been appointed to the acting secretary role in Mr Stefanic's absence. 

But Senator Hume said she planned to write to the attorney-general seeking assistance in reviewing the governance practices at DPS. 

Crossbench senator David Pocock wanted to know why a question about corruption had disappeared from a DPS staff survey. 

He told the hearing that in 2019, a DPS survey found only 53 per cent of staff thought it would be hard to get away with corruption, compared to 71 per cent in the broader public service. 

Ms Hinchcliffe took the question on notice and said she would report back why the question was removed in recent surveys.

One Nation senator Malcolm Roberts asked how staff morale had been affected by Mr Stefanic's absence, to which Ms Hinchcliffe said morale hadn't been affected. 

The hearing ended with Senator Hume telling Ms Hinchcliffe that at the next hearing she would be asking further questions about Mr Stefanic's leave and how much it had cost the taxpayer.