A specialist team - including the SPCA, Ministry for Primary Industries and Massey University - has been going door-to-door in Edgecumbe to search for animals.
The Bay of Plenty town has been evacuated after a Rangitāiki River stopbank was breached on Thursday. The breach has been temporarily repaired but Whakatāne's mayor said today people should prepare to stay away from their homes for a further 10 days.
SPCA senior inspector Liisa Jones said the team did know there were some trapped animals that were alive, and those would be the priority.
"Today, we're going to be going through the main deluge area, we're going to try to get every single animal out," she said.
"We do have some animals that are currently trapped there that we need to go and get and they're alive so they're going to be our number-one priority.
The team were also called in yesterday to rescue two cows that were drowning.
"We needed to go in and it took us two and a half hours for us to get them out - we actually had to swim in there to try and get them out."
"In regards to animals that are in dry areas we've got staff going in and leaving food and water for them, checking on them, we're removing them if we can.
Animals would be brought back to a welfare centre, where people would be able to be reunited with them, she said.
Anyone with animals they were concerned about was encouraged to call 0800 306 0500.