"Detailed survey assessments have confirmed that wooded structural elements under the deck need to be either repaired or replaced," AT said in a statement.
"However, the final design to make the wharf safe has identified costs currently above budget."
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AT's Portfolio Delivery Director David Nelson said they were working with a complex site and that the marine environment came with its own set of challenges.
"The most recent design effectively means we need to rebuild the wharf, so it's not the simple repair originally envisaged." he said.
"We want to make sure we get it right especially with the upcoming construction of the SeaPath and SkyPath".
North Shore councillor Richard Hills said it was "incredibly frustrating" to hear the news.
"They now say they need to replace the wharf not just repair the wharf which was never the case a year ago," he said.
"This is despite myself, Chris Darby, John Gillon and Dan Bidois constantly asking for assurances that the original plan was on track."
"We have all been concerned at the timeframe and asked if the budget was too tight but the expectation had stayed the same until now," he said.
He said another delay for the local community was "outrageous" and that AT should apologise for giving such high expectations.
AT recognised the wharf's place in the community, and the importance of reopening or redeveloping the wharf as soon as possible, it said, adding daily patronage for the Northcote Point ferry averages around 80 regular users.
