KiwiRail and the Dunedin City Council were in disagreement over which was responsible for raising the pathway surface, to be level with railway tracks which were lifted a few centimetres after maintenance earlier this year.
The gap had caused at least one Dunedin cyclist to fall off their bicycle and had frustrated others.
A warning was painted on the asphalt path to alert cyclists and pedestrians of the surface variation.
Although KiwiRail did the work which resulted in the surface level discrepancy, it asserted the council was responsible for maintaining the pathway.
But the council initially wanted KiwiRail to undertake the minor work, because it was the company's railway line maintenance which created the issue.
KiwiRail confirmed this week it was not responsible for maintenance of the pathway, despite its work on railway tracks.
"According to the terms of our lease agreement, all maintenance obligations for the cycleway rest with the council," KiwiRail senior communications adviser Jenni Austin said.
DCC transportation operations senior contract supervisor Peter Hughes yesterday said the council had accepted responsibility for fixing the pathway.
It would be raised to match the track level in the next few days, weather depending.
"There was some confusion at first. [KiwiRail] raised the level of their line and we were waiting to see if they were going to raise the surface of the path because they created the problem," Mr Hughes said.
The "minor" work would be undertaken by council contractors, with supervision from a KiwiRail official, he said.
Costs of the asphalt addition would come from the council's maintenance budget, Mr Hughes said.
"Our guys will go in there as soon as they can. They will fill the gap with asphalt, going about 2m across and half a metre back [from the railway lines] to bring it level to the [railway] sleepers that have been put in," he said.