The Wallabies are due to play the All Blacks in two Bledisloe Cup matches in New Zealand.
The Wallabies coach had complained about the lack of preparation time due to quarantine requirements.
Ardern told Morning Report the Director-General of Health Ashley Bloomfield was happy for the team to train together while in quarantine.
Training will be allowed from day three and the full squad from day six.
"The quarantine changes are more around whether or not the director-general is happy for teams to be training together while they are in quarantine. The answer is yes.
"What Ashley Bloomfield has said is training can happen in three days and he said because of the risk profile for Australia being lower relative to the other teams being talked about previously that full squads can also train together from the six-day mark so that means you can have full regular training whilst they're in quarantine."
She says it is about sticking to the commitment made to Australia.
"Everyone's pulling out all the stops to make it work."
Director-General of Health Ashley Bloomfield said he was asked for further advice yesterday by NZ Rugby chief executive Mark Robinson on the Bledisloe Cup matches.
"When we were considering the Rugby Championship we had teams coming out of South Africa and Argentina. We know that there have been positive tests among Argentinian players even in this last week or two.
"The Australian team is a different risk profile. Australia's got much lower rates of infection, all the players have been up in New South Wales for a period of time, and so these were the considerations that Mark Robinson asked me to have a look at.
"The risk profile is quite different if you're just looking at the Australian team then there is the opportunity to have some different quarantine arrangements, in particular for that second week of quarantine."
New Zealand's quarantine protocols were a significant factor in losing out to Australia in a bid to host the Rugby Championship.
One of the matches is likely to coincide with the general election on 17 October but Labour leader Ardern says she is not concerned about that.
She says the evening match will not impact the election, "not with early voting, not with voting during the day".
"Not a consideration I worry for us. Not worried by that all.
"I think New Zealanders are perfectly able to multitask with an election and a sporting match."
As for people watching the match instead of the poll's early results, she says "we could all do with a distraction in our lives at the moment".