The two nations promise to have each other's backs under the Pukpuk Treaty, named after the pidgin word for crocodile.
Prime Minister Anthony Albanese is in Port Moresby this week for the golden jubilee celebrations and hopes to finalise and sign the new pact on Wednesday.
He told reporters on Tuesday that the PNG cabinet met on Monday night to give final approval but didn't have a quorum because some ministers were back in their constituencies for independence celebrations.
But he expected his counterpart James Marape to sort it out quickly by ushering the process through his cabinet virtually.
Celebrations to mark PNG's independence from Australia wrapped up on Tuesday night with a mass gathering at Port Moresby's Sir John Guise Stadium.
In Canberra, the pact won support from Opposition Leader Sussan Ley.
"The new treaty being finalised by Papua New Guinea and Australia will bring a transformation of our mutual partnership - providing the basis of deeper ties for the next fifty years," she said.
The treaty will lead to the close integration of the two nations' defence forces and trigger mutual support obligations if either country comes under attack.Â
Mr Albanese said the idea that PNG would be attacked and Australia would sit back and watch is "something that wouldn't happen" given their history and close ties.
Mr Marape has said he had "a moral obligation to build my military to a level that I can have the capacity to defend Papua New Guinea, every child".
The landmark agreement will enable PNG nationals to serve in Australia's defence force with the same pay as other members and start a pathway to citizenship.
PNG Defence Minister Billy Joseph on Monday said the deal was a "mutual defence treaty" that would have the nations working together to defend each other's territories.
It is likely the deal will be seen with a more cynical eye across the Pacific, with many nations not well disposed to the militarisation of the region.
Mr Albanese's deal-making in the Pacific has been a central tenet of his government's foreign policy, including a landmark climate pact with Tuvalu and a migrant-dumping agreement with Nauru.
He is also pursuing a security treaty with Fiji, one of just three Pacific nations to have a defence force, along with PNG and Tonga.
In recent years, Australia has struggled to carve out security pacts with two other Melanesian nations - the Solomon Islands and Vanuatu - which maintain warmer ties with China.
The Greens have also raised concerns over the Pukpuk Treaty, including the degree of integration between the two forces.
"What, for example, would Australia's role be if there is a return to conflict in Bougainville?" defence spokesman David Shoebridge asked.
"Does it mean they follow us into a US war, or is it about military bases?
"Absorbing PNG's military into the Australian Defence Force is a very questionable way to celebrate the 50th anniversary of independence."
As a gift to mark their golden jubilee, Australia will help PNG build a new ministerial wing at its parliament.
