Principal Trina Eastwood said a child was almost hit on the Taieri Rd crossing, between Gilmore and Cromwell Sts, late last year, when a car failed to stop and shunted another car on to the crossing.
Following the incident, Mrs Eastwood asked police if improved signs could be put up.
But, instead, the pedestrian crossing was decommissioned this month and all signs and road markings removed.
Dunedin City Council senior traffic engineer Bruce Conaghan said the crossing was decommissioned for safety reasons.
He said a DCC survey was carried out following the near miss last year, and found on average only six people used the crossing daily.
Mr Conaghan said if a pedestrian crossing was not used by many pedestrians, drivers tended to get in the habit of not noticing the crossing because they were not used to stopping for it.
Its existence could not be justified and it was safer for the community if the crossing was decommissioned, he said.
"Regardless of what is there, people need to take time to look, listen and think before crossing.
"The school and parents could assist children crossing the road."
Mr Conaghan said there were no black and white striped poles, no signs, no white diamonds painted on the road and no zebra crossing.
"It's now quite clear that it is not a pedestrian crossing," he said.
"It will take people about three months to notice the changes and become accustomed to them."
Mr Conaghan said crossings were constantly being reviewed to determine their necessity, but there were no plans to close any other crossings at this stage.
Mrs Eastwood said the decision was "bizarre" and went against everything in the road code.
While staff at the school were upset about the decision, resident priest, Fr David Hercus, was concerned about the state of the crossing.
He said there was confusion about whether it was still a crossing or not, because an island remained in the middle of the road and the zebra lines could still be seen, even though they had been painted black.
A church parishioner was killed on the crossing about 10 years ago, and Fr Hercus was concerned someone else might be killed.
"It's very dangerous the way it is.
"Some people, both motorists and pedestrians, think it is still a crossing.
"It's not helpful for children to be on a crossing that is neither here nor there.
"It's in a nebulous state.
"What is it? Are you safe to cross on it?"Fr Hercus believed it would be safer if the crossing was controlled by traffic lights.
"That would be ideal."
Mrs Eastwood said the school would hold a road safety campaign for its pupils when school resumed next week, to make sure pupils were safe when crossing the busy road.
