Gisborne has issued a flood warning for the Waipaoa River near the settlement of Te Karaka.
Tairāwhiti Civil Defence said the river was likely to peak at 6 metres.
However, river level data on the council's website puts it at more than 6.8m at Kanakanaia at 11.30pm on Monday.
Waikohu Civil Defence is recommending residents of the small East Coast settlement evacuate their homes as the Kanakanaia River level rises.
It is also warning motorists not to go over the Puha bridge.
Heavy rain has hit the Tai Rāwhiti area and Civil Defence has also issued a flood warning for the Waipaoa River near Te Karaka.
The Mangatu Marae has opened to local residents who wish to evacuate.
Meanwhile, severe weather in the capital is causing headaches for passengers trying to cross Cook Strait over the next couple of days.
Interislander ferries have been cancelled due to the weather, with waves expected to reach four to five metres.
Sailings on Bluebridge show there are afternoon bookings on Wednesday to Wellington and none until Thursday for Picton.