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The tunnel, a main link between the city and the eastern suburbs, has been shut in both directions since 6am.
The two-car crash happened in Paterson St on the city side of the tunnel.
One person has critical injuries, while a second has moderate injuries.
A Wellington Free Ambulance spokesperson confirmed they transported two people to Wellington Hospital.
Motorists were advised to detour through Newtown or to head around the bays.
Buses were experiencing delays, and Wellington Airport is advising customers catching a flight to plan ahead.
Police said the single-vehicle crash happened just after 6am.
A spokesperson said fire crews freed a person who was trapped in a vehicle.
The Serious Crash Unit is on site.