Auckland councillors today voted out an option favoured by Team New Zealand that would have seen an extension of the Halsey St Wharf.
Two options, which would both see clusters of bases around the Auckland waterfront, will now be negotiated with the Government and Emirates Team NZ.
Team New Zealand said it was willing to be flexible about both options now available.
However, they were disappointed that the full Halsey Wharf extension option had to be taken off the table.
"It seriously restricts the ability for the marine industry to benefit from the berthing of the superyachts and the ability to extract maximum economic benefit," Team New Zealand said in a statement.
"The final plan for the Wynyard Basin option will need to reincorporate the lost superyacht berthage within the event perimeter.
"We will continue to work constructively with council and Government to progress the plans."
Councillors, local board members and stakeholders from the marine industry had earlier gathered to discuss and suggest options for an America's Cup base in the city.
The options were debated before the councillors' vote.
The options considered included extending the Halsey St Wharf to house up to eight yachting syndicates.
The other was spreading the bases along Halsey, Wynyard and Hobson wharves.
Community groups and members of the public were given an opportunity to put forward their own views about what they thought was the best option.
Team NZ today compromised and said they would back the Wynyard Basin clustered option across three nearby sites for the America's Cup bases.
They previously preferred Halsey Wharf, which would require extension into the harbour - as it would provide a more "village feel" to the event.
Board member Sir Stephen Tindall earlier said he was concerned about any more movement out into the harbour.
The cost of building in Wynyard Basin sits between the other two options at $130 million, and has the fastest construction time of 10 months.
Team NZ chief operations officer Kevin Shoebridge did, however, have some issues with the Wynyard Point dispersed option; including that at least two base spots would see a low-water issue.
He also said a dispersed base might lack a cohesive village atmosphere.
Speaking about how the event was hosted in San Francisco, he said: "It was pretty fragmented ... and it didn't draw a lot of the public because of that."
For the international crowd watching the event, it was fine, he said.
"Locally, it suffered. A lot of people in San Francisco didn't even know the event was on."
The Heart of the City also favoured clustering the bases and was vehemently opposed to the Halsey St Wharf extension.
A spokeswoman said clustered bases would be a more practical and ideal option that would meet the teams' needs as well as be economic and meet the public's needs.
The Waitemata and the Devonport-Takapuna local boards were also against extending the wharf into the harbour, but support having the Cup in Auckland.
Waitemata local board deputy chairman Shale Chambers said the clustered bases would be a "pragmatic solution" that would save up to $50 million and provide a legacy for the city.