The National Referral Hospital and many communities living near rivers and streams were flooded early this morning.
RNZ reports water filled up wards and corridors at the hospital leaving patients unable to move and causing concern about dangers with the electrical wiring.
People living near streams and rivers evacuated to higher ground fearing another flood situation like April 2014.
Those floods killed 16 people, left some 10,000 homeless and caused widespread damage.
Warnings have been issued for residents to stay indoors and move to higher ground if necessary.