CentrePort chief executive Derek Nind said the port was working with stakeholders to reach a decision on the buildings, which had suffered significant damage.
He said options ranged from demolition to repair but engineers were still completing assessments.
"As we've worked through that process we've become aware of the damage and... we're looking at alternative ways to work."
Other earthquake damaged buildings on CentrePort's land include Statistics House, Customhouse, Shed 39 and the BNZ building.
Economic Development Minister Steven Joyce has described Shed 35 as being on a lean and at risk of collapse.
Nind confirmed the heritage building was cordoned off and had suffered significant damage to its foundations.
That cordon has meant trucks carrying cargo from Bluebridge ferries cannot use their usual route through the port and on to the road.
Strait Shipping commercial general manager Ed Menzies said Bluebridge was fully operational but the cordon slowed the cargo loading process.
"We've gone from having dual access through to port roads down to a single entry and exit point, which is one way when we're discharging and loading the vessel."
Menzies said Strait Shipping was working closely with CentrePort on an alternative, which had two exit points on to the road.
He said the business relied on having a working exit route.
"Shed 35 is an impairment to that in the future, if it stays."
Wellington City Council chief resilience officer Mike Mendonça said the council was in the process of weighing up the heritage value of Shed 35 against other interests.
He said the council was not involved with other damaged buildings at CentrePort.
"Those buildings and other buildings on the waterfront are the building owner's responsibility. So, the city council's role, other than safety in public areas, is very limited."
In another part of the port a cruise ship terminal has been cordoned off because of significant earthquake damage.
Cruise New Zealand executive officer Kevin O'Sullivan said no cruise ships this season have been interrupted because of it.
He said shuttles were moving passengers off the ships and into the city because no one was allowed to walk on the wharf.
"Of course [CentrePort] is going to have to work on a day-by-day basis but at the moment there has been no cancellations, so hopefully that will continue."
A cold storage building at the port has also been cordoned off.
However, Nind said the biggest problem for the port was its container operation.
He said a crane had been busy re-stacking containers while road sweepers removed liquefaction around them.
"Now we're moving into the more medium-term problems and in the next three of four months we've got to solve some of those infrastructural challenges."
Nind said that meant finding a way to get container cranes operational again.