Onehunga Business Association manager Amanda Kinzett said the Transport Agency consulted on a 4.5m high wall in front of the historic Landing Hotel and other businesses, as part of the plans.
She said the wall would cut them off from access to the recently redeveloped $30 million foreshore and Onehunga itself.
"The port will be unusable. This is unacceptable to the community."
The NZTA said recent designs for the area include a lowered East West Link to allow better visibility for properties near the wharf.
Auckland highways manager Brett Gliddon said the East West project would not stop plans to redevelop the port. There are no plans to bulldoze or undo any of the work it recently completed as part of the regenerated and developed Onehunga Foreshore.
"As part of the project the Transport Agency will be providing very good access to the port area, not blocking access. Providing this access has always been part of the project plans.
"We are committed to and will continue to work closely with Panuku Development Auckland to progress a design which enhances access to the wharf, enables future development and considers the physical and visual impacts on the surrounding environment."
Editor of the Transport Blog, Matt Lowrie, said the project directly contradicted the New Zealand Coastal Policy Statement which says reclamation of land should generally be avoided in the coastal marine area.
In an update to council on the road's environmental impact, the NZTA said it required significant use of natural resources as it involved reclamation along the northern edge of the Mangere Inlet and several ramps.
The briefing said it was also likely to involve significant earthworks due to its 5.5km length.
The area is home to a number of unique ecosystems and is a habitat for national and international migratory birds with a number of locally extinct species which have re-established in the inlet.
In the document, dated July 6, the NZTA admitted: "The proposal will therefore likely result in significant, irreversible changes to the environment."
The design for the project won't be confirmed until the application is lodged with the Environmental Protection Authority in December this year.
There is likely to be further changes as the NZTA responds to the 135 submissions it received.