All Blacks discard Piri Weepu is the obvious player to call upon as cover but if both Ellis, who has damaged ribs, and Cowan, who has a broken nose and a knee strain, need to be replaced, half-back stocks start to look a little thin.
Below Weepu, New Zealand's leading half-backs Jamie Nutbrown, Alby Mathewson, second string New Zealand Maori half-back Chris Smylie and Taniela Moa have minimal international experience and the absence of Byron Kelleher (overseas) and the injured Brendon Leonard is keenly felt.
Ellis and Cowan will be reassessed on Monday, when any replacements are likely to be named.
New Zealand will need to be ready for another battle against Robbie Deans' Wallabies, who top the Tri-Nations standings after two wins from two games and who are likely to have captain Stirling Mortlock back.
All Blacks captain Richie McCaw has been back running for the past couple of days but no decision on whether he will make his comeback at Eden Park has been made and he will be assessed on a day-to-day basis.
Having McCaw back on the park would certainly be a welcome boost for the All Blacks as they look to stop the rot.
Assistant coach Steve Hansen believes the team are more than capable of turning things around in a week, pointing out that world champions South Africa bounced back from defeat in Wellington to claim their first win on New Zealand soil in 10 years the following weekend in Dunedin.
"We've got enough experience in the group to turn it around. When you break down (Saturday's) game we weren't that far away. We've just got to cut down the error rate and play a little bit smarter," he said.
"You just can't play as much rugby behind the gain line, behind the 10-yard mark in your own territory as we did. We've got to look at that and change it.
"The key thing is that we don't panic. What we've got to do as coaches is to keep our composure, keep our calmness.
"What we've got to do as a collective group is train hard but also very smart and make sure we turn up on Saturday a lot wiser than we were last week and also mentally and physically ready to play."