Coffins are "covered in water" at the Putiki cemetery.
The historic urupa, next to St Paul's Anglican Church in Anaua St, Putiki, has been closed because of serious problems with a rising water table.
Huia Kirk, from the St Paul's Church restoration trust, said the urupa appeared to escape flooding during the June floods. However, it now seems the water is coming up under the urupa.
"We start digging for a burial and there are things floating around in water. It's become a real problem for family plots when the coffins already there are covered in water," Ms Kirk said.
She said the urupa, which is close to the Whanganui River and is bordered on one side by the former bed of the Ngatarua Stream, had always had a problem with water, but it had become worse since the floods.