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Some may have also been erected without building consent.
Dunedin City Council building solutions principal adviser Neil McLeod confirmed the council had issued notices to itself regarding some bus stops not meeting building standards, or being built without consent.
Two notices to fix had been issued for shelters in Moray Pl and Cumberland St, he said.
However, Mr McLeod could not say how the failures had happened, or how much it would cost to fix it.
"We are aware there is a potential problem and we are investigating it."
Further information would be provided when the investigation was complete, he said.
Meanwhile, Bus Users Support Group Otepoti Dunedin co-president Alex King said the group felt the council had been moving slowly on improving bus shelters for "a long time".
There were many bus shelters that needed to be improved, or that were not there at all and needed to be, he said.
"We have been bringing this to the council’s attention for a long time. Surely it can not be an impossible task — it just seems like a failure of the whole system," he said.