"It's going to make life easier for the transport agency, which is good for them, but not good for Auckland," said one source about plans for a waterfront village, apartments and commercial uses at the wharf.
Another source said the deal will "shaft the good folk of Onehunga".
At midday today, Ports of Auckland spokesman Matt Ball said the plan was "not true".
Four hours later, Auckland Council, Panuku, the Transport Agency and the ports company issued a joint statement saying they are in the early stages of negotiations around the sale of the Onehunga wharf to the transport agency while the motorway is built.
The statement confirmed the wharf would then be sold to Panuku.
"All parties agree that this will be the best outcome for everyone involved and are committed to continuing to work together to enhance access to the wharf, enable development and create the best outcome for the community in terms of both transport links and urban development," the statement said.
Jackson said the port was the key to unlocking the Manukau Harbour and it had to be done properly. The fishing industry was interested in taking the area over and Panuku wanted to cover it in apartments, he said.
About $1.8b was about to be spent on the east-west link and no-one knew how it was going to connect into Onehunga. The transport agency had consent for a $25m pedestrian bridge and no idea how to connect it into Onehunga, plus there were environmental sediment issues, he said.
Panuku did not have the management skills to oversee development of the port area, said Jackson, who said he had only just been informed of the plan by transport agency highways boss Tommy Parker.
In November last year, Panuku chief executive John Dalzell said transforming the Onehunga port site for public use was key to unlocking the economic, recreation, tourism and transport potential of the Manukau Harbour.
The development is planned to complement a $30m development of the Onehunga foreshore, which opened in November last year.
At the time, Dalzell said Panuku had undertaken technical and environmental due diligence on the site and hoped to finalise a conditional sale with the port company within a few months.
Since November last year, the transport agency has firmed up plans for an east-west motorway costed at $1.25b to $1.85b. Plans show the motorway requires a large interchange around the Onehunga port area.