Jones is believed to favour the more experienced Rogers, who has played in every position for the Wallabies except scrum-half, in front of the younger MacKay, who has struggled recently with a knee injury.
"It's between those two," Jones said from Coffs Harbour, where the Wallabies are putting the finishing touches to their preparation before flying to Auckland on Thursday.
Meanwhile, hooker Stephen Moore has been ruled out of Saturday's Test with a lower back injury.
Moore, who complained of discomfort in his leg at training on Friday which is thought to be related to an existing lower back injury, has returned to Brisbane for an MRI scan and further tests.
His place in the squad has been taken by Adam Freier, who joined the team in camp in Coffs Harbour on Sunday.
Moore becomes the 17th player ruled out through injury.
Jones admits it is disappointing, but claims it does present a good opportunity for Freier.
"It's another injury and another disappointment, but Adam has already had a taste of Test rugby and is looking forward to capitalising on this latest opportunity," Jones said in an ARU statement.
"He's an enthusiastic player, and with another four or five new blokes in the squad at the moment there's certainly plenty of that out there in each session."