The breach near Lake Victoria could prevent the diversion of up to 10 gigalitres from the Murray.
SA State Emergency Service Chief Officer Chris Beattie said work was underway to try to repair the levee but if that was unsuccessful the extra water would flow into SA.
"Part of that lake system provides an avenue for us to divert water and the intent has always been to divert five to 10 gigalitres into Lake Victoria," Mr Beattie said on Thursday.
"Obviously, that knocks the edge off the peak flow. If they can't repair the levee...then we may see a lack of capacity to knock that five to 10GL off the peak."
Mr Beattie said it was uncertain whether repairs could be achieved and still retain the ability to divert flows.
The concern came as more warnings were issued for SA Murray communities with people at Walker Flat urged to evacuate immediately and a watch-and-act message in place for a 40-kilometre stretch of the river further upstream, taking in Caurnamont, Purnong and Bowhill.
By early Thursday, all residents in Walker Flat had left except one who had elected to stay.
The SES said a number of other levee failures had been dealt with including incidents south of Renmark, near Barmera and at Port Mannum.
A failure of the levee protecting the caravan park at Kingston on Murray had also forced the evacuation and closure of the park.
Up to 4000 properties in SA are forecast to be inundated by the water surging down the Murray, with more than 450 of those considered permanent residences.
About 1100 are thought to have been flooded so far.
The peak in water levels is expected to hit Renmark, near the Victorian border, between Christmas and New Year and then flow down to the lower reaches over the next few weeks.
Peak flows are still forecast to reach between 190 and 220GL a day.
Levee construction along the river is nearing completion with the last works expected to be finished in towns including Mannum, Berri and Loxton this week.
Most ferry services across the river have closed or been moved to higher ground.
The SA government has provided a $51.6 million assistance package, including support for tourism and other businesses, as well as direct emergency payments to homeowners.
Premier Peter Malinauskas acknowledged a level of community concern and uncertainty about rising river levels, compared to floods in the past.
But he said the river was a different place to what it was during the record floods of 1956 and the last big flood in 1974.
"This is the first time in over 50 years we've seen this volume of water coming our way. It's hardly surprising that the river is performing differently," he said.
"Think about how different our state looked in 1956. That is true for river communities as much as it is for the city.
"So this is very much an unprecedented situation. Floods, of course, have a precedent but floods in the modern era don't in this part of our state."
