The cyclone is weakening but heavy rain is expected to pelt parts of the South Island this morning.
The system was centred just east of Kaikoura at 5.30 this morning and is moving south.
MetService meteorologist John Crouch says bands of heavy rain have been affecting parts of Wellington, eastern Marlborough and Canterbury overnight.
He says those bands of rain will ease in Wellington fairly shortly this morning.
However, John Crouch says some bands of rain could continue to affect Canterbury and the Kaikoura coast through to mid to late morning.
He says localised falls could generate a bit of surface flooding in the Christchurch area.
South Island firefighters have gone to three Canterbury homes who have called for help with flooding as heavy rain drenches the region.
A Fire Service spokesman said this morning's flooding, which happened in Rangiora and Kaiapoi, was very minor and was only affecting land surrounding the homes.
"It's very quiet compared with what we were expecting," said the spokesman.