Scott Morrison has personally spoken to Defence Minister Linda Reynolds’ doctor about her extended medical leave.

Senator Reynolds has taken leave until at least April 2 as she faces intense scrutiny over her handling of rape allegations raised by former staffer Brittany Higgins.

The Prime Minister described Senator Reynolds’ condition as “quite serious”.

“I have, at the Minister’s permission, spoken to her doctor about this issue and it is a serious issue,” Mr Morrison said in Sydney on Tuesday.

“So we are supporting her in getting the physical health treatment that she needs over this period, that doctors have advised that she needs to take.”

Attorney-General Christian Porter has also taken indefinite leave after being accused of a historical rape allegation, meaning two of the eight national security committee members are absent.

Mr Morrison said both ministers were being temporarily replaced by highly competent cabinet colleagues and he was also maintaining “a very close watch” over their portfolios.

The Prime Minister has ordered an inquiry into what his office knew about Ms Higgins’ allegations.

The secretary of the Department of Prime Minister and Cabinet, Phil Gaetjens, is investigating which staff in the Prime Minister’s Office were aware of the alleged sexual assault.

Mr Gaetjens has not finished the investigation and does not know how much longer it will take.

“It depends on responses from individuals we have been interviewing,” he told a Senate committee in Canberra.

“I don’t think it will take too much longer but we have to go through due process there.”

Mr Gaetjens refused to commit to a timeline and when asked whether the inquiry was taking him away from other duties, including an analysis of coronavirus risks, he replied: “It means less time at home.”

Mr Morrison has refused to guarantee he will release the inquiry report once it is complete.

-AAP