NZTA staff met West Harbour Community Board chairman Steve Walker on Wednesday to discuss the fence, and yesterday confirmed their timetable to remove it.
It had been installed to prevent illegal rubbish dumping in the area, but the agency acknowledged other community uses of the area had been overlooked.
NZTA coastal Otago maintenance contract manager Nick Rodger said the fence was "not the best solution" but there were no immediate plans to replace it with something else.
Instead, members of the public were encouraged to report any problems with illegal dumping in the area.
Mr Walker said the decision was "an excellent outcome".
"To be honest, I wish everything was actioned this quickly," he said.