Two Interislander sailings between Picton and Wellington were cancelled on Sunday, while two further sailings were delayed by hours on Sunday night due to the swells.
One of those was the Kaitaki, which was due to leave Wellington at 8.30pm with more than 800 passengers on board.
In an email sent to passengers just after 10pm, seen by RNZ, Interislander apologised for the inconvenience of the delay.
"We will be commencing loading asap but will not be leaving Wellington until the Master is comfortable to depart due to rougher sea conditions than forecast - this could be at least 4 HRS," the email said.
"If you wish to not travel tonight please advise staff but keep in mind that our ships are fully booked for the next week."
The Kaitaki finally set off about 1am on Monday, according to ship tracking website MarineTraffic.com.
The Kaiarāhi, which had 500 passengers on board, was also delayed for hours before setting off from Picton just before midnight Sunday.
Further disruptions were in store on Monday, with two sailings of the Aratere - at 6.15am from Wellington and 11am from Picton - cancelled.
However, scheduled Kaitaki and Kaiarāhi sailings were expected to go ahead, a spokesperson said.
Meanwhile, Bluebridge had cancelled four sailings on Sunday, and five on Monday, with further cancellations likely.
It said conditions were likely to remain unsettled until Monday evening.
"Customers impacted by these cancellations will be contacted by our team for alternate sailing options."
