People in Edgecumbe have been advised to leave their homes immediately.
Welfare centres had been set up in Kawerau and Whakatane.
They were located in Firmin Lodge in Kawerau and the Whakatane War Memorial Hall.
The council said there were between 500 and 600 households in the flooded township with a population of around 1600 people.
The rural area around Titoki Rd to the west of Whakatane had also been evacuated due to the overtopping of a floodbank on the Whakatane River.
The Whakatane and Rangitaiki Rivers were at historically high flood levels and river flows were unlikely to subside sufficiently to allow access to cut-off areas in Taneatua, Ruatoki and Waimana for some time.
Evacuated residents are being told they may need to be out of their homes for the next 72 hours.
Anyone who requires urgent assistance is advised to ring emergency services on 111.
Police and firefighters were in the area helping arrange transport for residents.
State of emergencies were lifted in Whanganui and Rangitikei districts this morning after the flood threat passed.
Whanganui District Council has warned motorists to be careful on their roads for the next few days.
"The Whanganui District is experiencing strong and gusty winds and ground conditions are currently saturated. These winds may cause trees to topple, further slips and road dropouts.
"We urge drivers to take great care. Stay safe out there."
