A scheme crucial to both ends of a "lifeline" sea link remains in limbo after it failed to win wholehearted backing.
Penzance Town Council last month issued their vision for the upgrade of outdated harbour facilities for the Isles of Scilly ferry link.
Cornwall Council has now responded and, while expressing support for the principle, important differences have emerged.
Alec Robertson, leader of Cornwall Council, voiced concerns that the town council's scheme would require changes to the harbour revision order – the structural framework within which work can be delivered.
He said this could violate a deadline for funding imposed by the Department of Transport.
Chris Ridgers, the council's portfolio holder for economy and regeneration, said they would support some of the proposals.
However, he added: "While the planning and consequential financial issues mean we cannot support all of the measures within the town council's scheme, we are keen to support as much as we can."
Mr Robertson said the deadline was looming. "The Department of Transport has been clear that the window of opportunity for securing public finding for a scheme for Penzance and St Mary's harbours is very short and, therefore, any scheme has to fall within the works approved by the current harbour revision orders," he said.
"The scheme developed by Penzance Town Council will require a fresh harbour revision order for Penzance which will defeat the funding application.
"Clearly we need to avoid this outcome.
"An opportunity exists for us to secure the Scilly's link through a scheme acceptable through the Department for Transport and which meets their requirement that it is deliverable within existing consents.
"This will require an amendment to a part of Penzance Town Council's scheme and we have written to the Town Council indicating our willingness to promote this scheme jointly with them."
Jon Pender, Penzance town councillor and chairman of the Penzance Harbour Scheme Management Board, said he was not discouraged by the response.
"There are different legal views," he said.
"Their legal advice is that another harbour revision order is needed. The advice we have had is different."
Mr Pender said he felt their plan had been flexible enough to allow room for manoeuvre.
But he added that the town council needed to digest the response.
"This is still do-able within the time frame. We have got to sit down and talk about what we can come up with."
The Council of the Isles of Scilly said it was encouraged by Cornwall Council's words of support.
Chairman Mike Hicks said he was "looking forward to working closely with Cornwall Council and Penzance Town Council on the proposals for Penzance Quay and St Mary's".
