John Faulkner faces significant challenges in his new role as defence minister, Deputy Opposition Leader Julie Bishop says.

Senator Faulkner was the "obvious choice" for the job, vacated by Joel Fitzgibbon, because he is an experienced parliamentarian.

The first challenge, she told Sky News, was "to restore the trust between the minister's office and the department".

Another was to restore morale within the defence forces, she said.

Senator Faulkner also had to implement the "incoherent" white paper on defence and find $20 billion in savings.

Ms Bishop says Prime Minister Kevin Rudd was forced to remove Mr Fitzgibbon from the line of fire.

Mr Rudd on Thursday said he had accepted Mr Fitzgibbon's resignation after it emerged the then minister had failed to disclose meetings he organised between Defence health personnel and the medical benefits fund NIB, which his brother heads.

"We certainly had more questions, more lines of inquiry... over his (Mr Fitzgibbon's) behaviour going back months," Ms Bishop said.

"This is a minister who has very questionable behavioural issues... and competence."

A battle with Defence over a pay bungle for special services soldiers gave the impression that Mr Fitzgibbon was not in control of his department, leaving him under siege in parliament for a few days earlier in the year.

Mr Fitzgibbon accused the department of incompetence because it could not provide assurances it had fixed the mix-up.

He also came under fire for a string of failures to properly declare gifts, including two trips to China provided by family friend and Chinese businesswoman Helen Liu, and a night's accommodation provided by NIB.

Defence launched an inquiry after it was claimed the department had mounted an unofficial investigation into the minister's association with Ms Liu. It concluded no such unofficial investigation took place.

AAP