Metservice says more heavy rain is expected to hit Hawke's Bay and Gisborne late Wednesday night.
Rain earlier on Wednesday caused floods and slips and closed some roads.
Civil Defence in Gisborne says it advised three families from the Mangatuna area, north of Tolaga Bay, to evacuate their homes on Wednesday afternoon, and two had done so.
It says the remaining family should be safe from flooding as river levels have dropped and should be able to cope with Wednesday night's rain.
The Transport Agency says a slip has closed State Highway Two at Tutira between Napier and Wairoa.
It says contractors will work through the night to get it open.
Civil Defence emergency manager for Hawke's Bay Ian McDonald says drivers need to be cautious.
The two regions have seen up to 160mm of rain in places over the last 24 hours, and Metservice is expecting localised downpours of up to 25mm an hour later on Wednesday.
It says there is a possibility the bad weather will die down on Thursday before returning in force on Friday.
Up to 180mm has fallen in some parts of the region.
The Waimata River, which runs though Gisborne, and the Hikuwai River, which flows through Tolaga Bay, are both at alert levels.
There is surface flooding on several roads, but the main state highways remain open.
Gisborne controller Jon Davies says two rural schools, Ngatapa and Tolaga Bay area school, are closed.
Gisborne Girls High School is also closed because the weather has damaged its sewerage system.
Strong winds and heavy rain are also expected in the central North Island.
Taupo Civil Defence emergency manager Phil Parker told Morning Report that trees toppled by strong winds two weeks ago are still being cleared.
He said people travelling through the region at the weekend should be prepared for delays.