Alan Tudge stands aside after Rachelle Miller alleges their affair was at times ?abusive?

The federal education minister, Alan Tudge, will stand aside while an investigation into allegations made by his former staffer is carried out.

The prime minister, Scott Morrison, on Thursday announced an investigation - to be carried out by the former bureaucrat Vivienne Thom - into the allegations Rachelle Miller made regarding her 2017 relationship with Tudge.

"These issues are obviously deeply concerning and I know deeply distressing - for Ms Miller, minister Tudge and the families affected by these events," Morrison said in parliament.

"I have discussed Ms Miller's statement with Mr Tudge, who refuted the allegations made. Given the seriousness of the claims made by Ms Miller, it's important these matters be resolved fairly and expeditiously.

"To this end, the minister has agreed to my request to stand aside while these issues are addressed by my department, through an independent and fair process."

The prime minister said the process would "enable my department to provide me with any further advice regarding any implications for the ministerial standards".

"But I wish to stress that this action in no way seeks to draw a conclusion on these matters," he said.