Dutch elm disease has been discovered on a tree outside the Auckland Art Gallery and on a group of elms in the historic Symonds Street Cemetery.
The fungal disease can spread quickly and is almost always fatal, says Auckland Council arboriculture and eco specialist, Simon Cook.
Trees have to be removed in order to prevent further spreading.
"While we are incredibly disappointed to have to remove these beautiful trees, we unfortunately have no other choice," Mr Cook said.
"We are committed to safety and respectfully removing the infected trees, then we will work to determine what may be suitable replacements."
Auckland Council has arranged for the elm tree on Wellesley Street outside the gallery to be removed on Sunday.
Due to the significant and sensitive nature of the Symonds Street Cemetery site, and the fact that several trees will need to be removed, Mr Cook said "a thorough methodology" for the removal project is currently being worked through.
First found in Myers Park over the 1989/90 summer, Dutch elm disease is currently restricted to the Auckland region. Recently, trees have become infected in larger numbers in central Auckland.
Mr Cook said to watch out for any signs of wilting, curling, or yellowing leaves; or dying or dead branches on elm trees around Auckland.
It is then the responsibility of the individual landowner to have the tree removed.