KiwiRail requires the 1.4m fences to be built on the new cycle and pedestrian path due to its proximity to rail tracks.
Port Chalmers resident Adele Woolley said she had enjoyed the harbour view while travelling to and from Dunedin for almost four decades.
"I have seen numerous schools of dolphins, seals and even orca during my daily commute," she said.
She believed the fence would "obliterate" any view of the harbour from St Leonards to Blanket Bay.
"I can only assume that those responsible for its construction have not considered its considerable negative visual impact."
Trains were infrequent, and until now common sense had prevailed in keeping people off the tracks, she said.
She believed construction by path builder Waka Kotahi NZ Transport Agency should be reviewed, and at the very least, the height of the fence should be reduced.
Agency senior project manager Jason Forbes said the fence was required by KiwiRail.
"It serves multiple purposes but safety is the primary one, to separate the path from the main trunk rail line."
The first 5km of the path from Dunedin to St Leonards had been in place for 10 years and also had a rail separation fence.
"Anywhere that the path is adjacent to the rail line, a separation fence is required; and anywhere there is a risk of falling, a protection fence is required," Mr Forbes said.
All fences were required to be 1.4m.
People would be able to see through the chain link mesh, he said.
Several fences were being built along the route.
While the first would be completed before the end of this year, others would not be finished until mid-2023.
KiwiRail operations executive general manager Paul Ashton confirmed the organisation required fencing in locations where public pathways were being built in the rail corridor.
"Safety is — and must be — our top priority," he said.
