However, Bluebridge announced it would run four scheduled services today and tomorrow with the rest of its regular services being cancelled.
It said its scheduled 8am Wellington to Picton service would run, but was now delayed from 8am to 11am.
The 2pm Picton to Wellington service would also run but was now delayed until 5pm.
Two freight only sailings will also depart Wellington at 11.30pm and Picton at 5.30am.
Regular Wellington to Picton sailings at 2.20am, 1.30pm and 8.45pm have been cancelled.
The 8am and 7pm Picton to Wellington services have also been cancelled.
Bluebridge has apologised for the inconvenience.
It said it was in the process of contacting customers affected by the delays and cancellations.
"We are offering full cancellation and refunds on all tickets for travel," it said on its website.
"If you would prefer to cancel, please call us on 0800 844 844 or email your request with your booking reference number to bluebridge.bookings@straitnz.co.nz."
The incident yesterday morning left dozens of trucks - some full of fresh produce - unable to get to their destinations.
A witness at the Picton end said he had been stuck in a queue of trucks for eight hours.
Interislander ferries were unaffected, the Herald was told.
A spokeswoman for Countdown supermarkets said the company's South Island stores were experiencing "some minor delays" in the delivery of products.
"Our Christchurch distribution centre primarily services our South Island stores," she said.
"So while we're seeing some minor delays due to the ferries, we're not expecting this to greatly impact product availability for customers."
A driver who had been waiting all night on the Picton side for his truck to arrive said he had been told people were scrambling to get their vehicles on to the Interislander but that service was already fully booked.
He understood strong winds last night may have been the cause of the ferry clipping the berth.
