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The man, who has interim name suppression, was charged with dangerous driving causing injury, and possession of an offensive weapon after the incident earlier this month. He also faces a charge of failing to stop for police, but it is not clear whether this relates to the tunnel ordeal.
The 31-year-old is alleged to have crashed into another car while driving the wrong way on State Highway 1 on the city end of the tunnel about midday.
Allegedly armed with a knife, he then climbed on to the pipes above the tunnel and stayed there for the next 10 hours.
Police closed the tunnel and spent the afternoon and evening trying to negotiate with him, during which time he refused anything to drink or eat and cut himself with the knife.
He eventually came down around 10.30pm and was taken away to be medically assessed.
Though it was the second call of the matter, today was the first time the man appeared in the Wellington District Court.
At the first call, the man was being held in a psychiatric unit in hospital. He spent about a week in hospital care after the incident.
Defence lawyer Georgia Pickering today applied for interim name suppression to continue.
The judge granted the suppression order.
He remanded the man on bail without plea until March.
At the time of the incident, Wellington District Commander Inspector Chris Bensemann said the number one priority during the incident was ensuring the safety of officers, the public and the people involved.
More than 20 staff including AOS, police negotiators and dog teams assisted and all possible tactical options were considered to safely resolve the incident.
"In the end this became a matter of patience and communication and we are glad the incident was resolved without further injury," said Bensemann.