The federal funding boost will upgrade bases in the Northern Territory, Western Australia and North Queensland during the coming decade, as part of Defence's pivot towards the Indo-Pacific.

Darwin's Larrakeyah Defence Precinct will be upgraded to berth submarines, but Mr Conroy said Australia's future nuclear submarine fleet would not be based in the Top End.

He said the government was focused on "hardening and developing" bases in the Northern Territory, as well as other installations in northern Western Australia and North Queensland.

"The NT is critical to the defence of the nation, not just in defending Australia but projecting power out into our region against any potential adversary," Mr Conroy said. He said the funding would go towards projects such as surveillance aircraft based at RAAF Tindal, near Katherine, and the purchasing and training of crew for new amphibious landing craft based in Darwin.