A top government security official remains on full pay despite being asked to step down while an investigation is underway into his leaked text messages to a Liberal powerbroker.

Home affairs department secretary Michael Pezzullo remains on his full package of almost $915,000, the new acting secretary Stephanie Foster confirmed.

Her pay packet has also gone up while in the role due to higher allowances.

The new boss expressed her shock at Pezzullo being stood down while the public service commissioner investigates his leaked texts.

“I want to start by acknowledging the significant shock all of us in the home affairs portfolio experienced … when secretary Pezzullo was asked to step aside,” Foster told senators in her opening statement to a parliamentary hearing on Monday.

“(It’s been) a difficult four weeks in the face of sustained and often distressing media reporting.”

The leaked messages revealed Pezzullo used a political back channel to two former Liberal prime ministers through powerbroker Scott Briggs to wield influence.

It included suggesting ministerial sackings and which MP should become minister of his department.

Foster said it had been an incredibly tough time for the organisation.

She said Pezzullo regularly disclosed conflicts of interest but didn’t confirm whether his relationship with Briggs was disclosed due to the ongoing investigation.

The public service’s policy states possible conflicts of interest include political affiliations and activities.

It is not suggested the messages show corrupt or illegal conduct but public integrity advocates have alleged Pezzullo overstepped the required impartial nature of heading a government department.

Texts show Pezzullo suggested now Opposition Leader Peter Dutton should become the new home affairs minister the night before Scott Morrison took the prime ministership from Malcolm Turnbull in 2018.

– AAP