More than 100 dairy farms in Southland and South Otago are being severely impacted by the extensive flooding in the region, said DairyNZ.
The area has been hit by severe rain and the river has now breached at high tide.
State of emergencies are in place for Southland, Fiordland, and Clutha.
DairyNZ's South Island manager, Tony Finch said while the scale of the damage was unknown, the affected farms were either under water or cut off with access roads flooded.
"We're in phone contact with many of the farmers. It's a dire situation for many right now. Their key focus is to get their people and their animals to safety," said Finch.
"Farmers and their teams are moving their cows to higher ground where they can, and we know of some who have been able to relocate their herd to their neighbour's farm out of the danger zone."
Dairy farms in the Southland-South Otago Oreti, Aparima and Clutha river catchments were the most severely impacted with the flooding and many areas are now also without power.
With access to the farms cut off, dairy companies are not able to get tankers in to collect milk, which means many farmers will need to dispose of the uncollected milk.
"Added to this, the flooding has impacted effluent management systems on many of the farms so farmers now also face the challenge of how to dispose of this in the best way."
Farmers in the affected regions were working together to accommodate animals on any dry land there is.
"We're also talking with farmers where the milk tankers can reach them, and many are sharing their milking sheds with neighbours who're flooded."
As well as farmers helping each other, Finch said impacted farmers could contact DairyNZ for help and advice.
"Adverse events like flooding create a lot of stress. I urge any farmers or farm team members who need support to give us a call, or contact the Rural Support Trust. Any farmers needing advice on managing effluent should get in touch with their local councils."
Meanwhile Rural Communities Minister Damien O'Connor is travelling to Southland today to assess the damage.
"I'm heading down there to support response and recovery efforts and meet with the locals' ',said O'Connor.
"A lot of people have been evacuated from their homes, have suffered flood damage to their properties or are disrupted by road and school closures. I urge people to put safety first, listen to the advice of authorities, and look out for each other."