The deluge caused widespread flooding, slips, surface damage and trees to fall across tracks.
The Department of Conservation (DOC) said most tracks were able to be reopened by mid November but some were harder to access and required boats or helicopters.
The Tunnel Beach short walk and carpark has been closed due to at least 10 large slips, with some travelling from the track down to the ocean.
DOC Coastal Otago operations manager Gabe Davies said the popular track was a priority as it received more than 150,000 visitors a year and also sustained the most damage.
It was a real shame as the department had only recently finished a new track alignment before the torrential rain hit, he said.
DOC was seeking geotechnical advice on the slope stability before any work started, which would also ensure the track was routed the right way.
It was expected to cost upwards of $160,000 to repair the track but that did not include up to $15,000 in gravelling to completely remediate the flood damaged surfaces if DOC had the budget for the work.
Some visitors continued to ignore safety advice and the road closed signs to walk the track, sometimes blocking residents from accessing their properties, he said.
"We know how popular this site is, but we want to make sure that when we do open it that it's safe for people to fully enjoy and experience, and at this time, we can't guarantee that," Davies said.
"We just don't think it's worth anyone's safety to risk not adhering to our guidance and the (Dunedin City Council's) guidance that the carpark and the track are closed."
Currently, DOC staff were not going onto the track because it was not safe, he said.
He has not ruled out a staged approach to reopening, but said it was important to ensure they futureproofed the track for future floods.
"We're working hard as a team to make sure that what we do come up with as the solution is a long-lasting solution."
But there had been some positive impacts from the closure.
A rare coastal turf that was often trampled by people walking on the headland - where Davies said they were not meant to go - was recovering.
"We've actually seen some of the different bird life, nesting out on the headland, which naturally we don't see when people are heading out there," he said.
So far, more than 200 hours of labour had already gone into trying to restore damaged Otago tracks and $4000 in materials.
People are urged to check the DOC website before using tracks and use caution while repairs were underway.
