Daniel Vickerman (shoulder) and David Lyons (groin) are both unavailable for selection and will undergo surgery over the next week, while Chris Latham has also been ruled out with a hamstring injury.
Fly-half Elton Flatley has at this stage been included in the squad, but with further medical advice still pending on his blurred vision, a decision on his availability is not likely to be made until later in the week.
It's better news however for Matt Giteau, Mark Gerrard and Clyde Rathbone, with all three players named in the squad.
"The injuries have been well documented over the last week or so, but that's rugby, and it just throws up new opportunities for the team and individual players," said Jones.
"At this stage, Matt Giteau, Mark Gerrard and Clyde Rathbone are all responding well to intensive treatment, while we will know more about Elton Flatley later in the week.
"It's a bit early to say just who will be available when we name the team next Wednesday, but they are all in the squad and will be given every chance to recover and prepare for the Auckland Test."
With four new faces set to join the Wallabies in Coffs Harbour, Jones claims it's an exciting and challenging time for the team.
"In a strange way it's quite exciting at the moment. Through circumstance we get the opportunity to bring some new and young talent into the squad and I know they are all keen to make the most of their opportunity," Jones said.
"We've also got just over a week to prepare for the last Test of the Tri Nations. It's a challenge we are looking forward to and one we are prepared for."