An X-ray revealed it had eaten stones too large to pass through its digestive tract.
Mr Lester said the bird would be be rested until Friday to recover from the anaesthetic before vets would try to extract the stones.
If the stones were too large they will be surgically removed.
Mr Lester said as soon as wildlife rangers latched onto the fact Manukura was not well it was bundled up and taken by car to the zoo.
The discovery the prize bird was ill had left staff at Pukaha feeling "distraught".
"But I think they are more hopeful this morning," Mr Lester said.
The kiwi had been taken to Wellington, instead of Palmerston North, because of the stranded cargo ship at the Port of Tauranga.
"We would normally take birds to the vets at Massey but they are all up north helping with the Rena crisis," he said.
Mr Lester said when Manukura returned to Pukaha it was likely to be taken off display for a while to allow the bird to quietly recover from the ordeal.
Manukura has been the biggest attraction at Pukaha since the days takahe were first housed there.
Mr Lester said its arrival, and the worldwide publicity that followed the hatching, had greatly boosted visitor numbers.
He said not only DoC staff but also iwi and the people of New Zealand felt a very strong attachment to Manukura.
The white kiwi was was an immediate sensation after being born at Pukaha in early May.
For weeks the sex of the kiwi was unknown but eventually it was determined to be female.
Manukura is not an albino but an all-white kiwi, believed to be the first since European settlement.
Before falling ill this week, the bird had been making steady progress and had reached a kilogramme in weight.
Mr Lester said everyone who cared for Manukura was remaining positive and hopeful for a recovery.