About a third of the area was affected by the deluge.
Queenstown Lakes District Council said it knew how distressing it was for families.
The council said that while people might want to check graves, they were asking them to stay away for their own safety.
"I can understand why family members would want to go up there and see their loved ones' resting place is still intact, but just give us a couple more days," Queenstown mayor Glyn Lewers said yesterday.
Fencing was being erected around the affected area, which would allow the rest of the cemetery to reopen.
Lewers said authorities were treating the site with the care it deserved and engaging with mana whenua and the faith based community.
An historic monument was impacted by the debris flow, but it was newer areas of the cemetery that were mainly affected.
A state of emergency was lifted in Queenstown yesterday, after heavy rain hit the area earlier this week.
Nearly 90mm of rain fell over a 24 hour period in the town, resulting in flooding and slips, which forced more than 100 residents from their homes.
