Swells up to eight metres, and 50-knot winds in Cook Strait overnight have delayed four ferries considerably this morning.
Strait Shipping's Straitsman and Santa Regina and InterIslander's Arahura and Aratere continued sailing through last night's southerly gales.
Interislander's Kaitaki is still in Nelson undergoing refurbishment work and is expected to return to Wellington over the weekend.
NZTA spokeswoman Lucy Corrigan said the Rimutaka Hill Road and the Desert Road remained open overnight but motorists were being warned to take care as both had icy driving conditions.
Meanwhile, trains on the Johnsonville line are running about 10 minutes late this morning, due to slippery track conditions, a KiwiRail spokesman said.
The East by West Wellington Harbour ferry service was back in operation this morning after sailings were cancelled due to strong southerlies overnight.
MetService Meteorologist Stephen Glassey said the low pressure system which brought rain to the North Island and top of the South Island over the last two days would move away to the east today, leaving a cool southerly flow in its wake.
"This should mean a fine weekend for many places, although the east and south of both islands can still expect cloud and a few showers.
Showers and a bitterly cold southerly were expected to ease throughout the day in the Wellington region today but the southerly winds would once again become strong overnight.