The crossing in Isis St closed on Wednesday last week after a KiwiRail audit, the council's network operations engineer, Mark Renalson, said.
He said the "well-used'' crossing would be closed for "a few months'' before work could be completed to bring the crossing up to national standards.
"They [KiwiRail] don't want to see it closed and neither do we,'' he said.
"We've got plans of specifications. It's just a matter of how we can apply it to that area, because of course it's not flat, there are stairs down to it and stairs up from it.
"This is not something that we planned for as far as forward funding is concerned, so we have to . . . get a plan, approve it, get a price, get some funding, get it done.''
A KiwiRail spokesman said, in an emailed response to questions, KiwiRail had been checking the safety of level crossings for a number of years.
Ministry of Transport figures show three deaths in level crossing accidents and seven injuries in level crossing accidents across New Zealand in 2015.
The spokesman said the 2015 figures "were very similar to the average deaths and injuries at level crossings for the previous five years''.
"As part of the compliance check, a small number of pedestrian crossings have been closed for safety reasons. Some of these are temporary closures to provide time for the relevant local authority to work with KiwiRail on putting the correct safety controls in place. It is expected that only two of these crossings will be permanently closed.
"So far, no crossings have been identified for permanent closure in Otago.''
In the South Island, the only sections of track remaining to be checked are south of Timaru, excluding Dunedin and Oamaru which had been checked, the spokesman said.
The national standards were issued by the New Zealand Transport Agency in 2012.
