The site is designated for a 5ha headland park at Wynyard Point, although the council has proposed realigning the park down the eastern edge.
An assessment of environmental effects from consultants UNIO Environmental says moving the ferry and fishing activities fits with the strategic direction in the Waterfront Plan and the overall effects would be minor.
Planner Dr Joel Cayford said the council was seeking to unpick the Wynyard Quarter urban design framework to free up space for the America's Cup bases.
He said a key principle of the design framework was a gritty working waterfront with the fishing industry being central and one of the reasons Wynyard Quarter had won international awards.
Last year, the development arm of Auckland Council said the cost of negotiations, relocation and new infrastructure for moving the fishing and ferry operations was $18m.
"The detailed costs will be worked through as the detailed designs are completed," a spokeswoman for Panuku Development Auckland said today.
The second application is for a cluster of bases on a 75m extension to Halsey Wharf, a 75m extension to Hobson wharf, and on the eastern side of Wynyard Pt wharf.
Meanwhile, Economic Development Minister David Parker and Auckland Mayor Phil Goff are continuing discussions about Parker's preferred land-based solution for the bases.
It is understood this involves moving the larger double-boat bases to Wynyard Point and having the single-boat bases on Halsey Wharf. This could reduce the Halsey Wharf extension from 75m to 25m.
Parker and Goff held talks yesterday. Neither politician would comment today on progress or say when a final decision would be made.
Submissions on the consents are open until February 28.
The resource consent for the wharf extensions can be seen here.