Climate-change portfolio leader councillor Tamatha Paul said it was unclear exactly what the funding was for.
"With all the crises we are experiencing - Covid-19, climate change, and failing infrastructure - we should be crystal clear about what we are allocating $76 million towards.
"This loan must be removed as a clear signal to Wellington that we are dedicated to climate action and that we will hold some of the biggest polluters in town to account."
Long Term Plan Committee chairwoman Sarah Free said she found the situation strange.
"Is this a replacement of the wall? Or is this an extension that might help with an extension?"
The loan has been removed from the current draft Long Term Plan, a budget that is reviewed every three years. The council could still revisit the loan in future budgets.
Wellington Airport CEO Steve Sanderson said they were "mystified" by the decision.
He said the council has been debating the wrong issue by conflating the seawall project with the runway extension.
"We are disappointed councillors chose to make this decision without consulting the Airport and without accurate information.
"We would have been happy to discuss these matters with councillors but were not approached or advised of the intention to raise this matter at today's meeting."
Sanderson said they will assess alternative funding.
"The sad thing about these ill-considered decisions is that the long-term infrastructure needs of the city are at stake. The impact on airport infrastructure should be the least of the Council's worries, when it is Wellington's main sewerage connection to Moa Point and key roading links to the south coast that are most affected. "
Paul said it was surprising and disingenuous for the airport to claim they are mystified.
"The airport was on notice about this when the Council declared a climate emergency."
The city council owns 34 per cent of the airport and Mayor Andy Foster is a board member.
Councillor Diane Calvert argued the seawall was something both the city and airport needed.
"If we don't have a functioning, safe, and quality airport we may as well give up our capital status now."
Councillor Nicola Young said the council needed to work with its partners rather than just "sticking it to them".
But she said the way the situation transpired was "mystifying".
Young said they should have had a briefing and Foster let them down.
Foster called a point of order: "You're assuming I knew about it," he said before winking at Young, who then pointed out he was a board member.
Councillor Fleur Fitzsimons said the whole debate raised the issue of whether it's appropriate for councillors, or in this case the mayor, to have "this type of commercial director role".
Councillor Jenny Condie said as a responsible shareholder the council needed to act in good faith and give the airport a chance to provide more information.
"But also put them on notice to say we want to have a serious conversation about this."
Councillor Sean Rush said he was uncomfortable with state funding going into something that could easily be financed by the private sector.
But he said he trusted officers that better information on the proposal was on the way.
Councillors agreed to hold a workshop with the airport on the matter during the Long Term Plan's consultation period.
Council officer advice said the seawall project differed from a previous budget line item for a runway extension, which was $90 million, because the sea wall cost was less and it was loan rather than a grant.
Before the vote, a Wellington Airport spokesperson said the $76 million was tagged to the seawall upgrade and not the runway extension.
The seawall upgrade needs to be done irrespective of the extension, they said.
"It is essential for resilience, safety and infrastructure protection. The seawall protects council assets including Wellington's main sewerage connection to Moa Point, roading between Lyall Bay, Breaker Bay and Moa Point.
The confusion around the funding set alarm bells ringing earlier in the meeting and prompted lawyers, advocacy groups and climate activists to argue their case against airport expansion plans.
Guardians of the Bays representative Tim Jones said a runway extension was "utterly unacceptable" in a climate emergency.
"Wellington City Council should have no part in funding it, however the funding is described in the Long Term Plan."