The reforms will push Australia closer to the centralised models of New Zealand and Ireland, where provinces answer to the national body on high performance decisions affecting test rugby.
On Tuesday, RA said the New South Wales Waratahs and the NSW Rugby Union (NSWRU) had become Australia's first Super Rugby club and member union to formally commit to the integration plan.
However, other member unions have pushed back on handing over commercial control.
No Australian team has won a Super Rugby title since the Waratahs in 2014.
RA have yet to decide who will run the integrated high performance programme or take over the Wallabies from Jones.
Persons:
Phil Waugh, Waugh, Eddie Jones, Jones, Ian Ransom, Peter Rutherford
Organizations:
MELBOURNE, Rugby Australia, Wallabies, New South Wales Waratahs, NSW Rugby Union, Super Rugby, Waratahs, Australian Capital Territory Rugby Union, Brumbies, Rugby, Irish Lions, Thomson
Locations:
New South Wales, NSW, Australia, Zealand, Ireland, Sydney, rugby, France, Melbourne