The $40m (€33.4m) figure is based on an assessment of immediate farm losses by Dairy Farmers of America (DFA) in the affected areas of Louisiana, Mississippi and Alabama. The effects of Hurricane Rita are not yet known.
Jim Hahn, head of DFA's Southeast division, said the dairy sector was uniquely vulnerable because fresh milk goes off so quickly.
"Cows don't take a rest when such tragedies occur, so the costs related to lost milk production and cow health begin to mount quickly," he said, adding that he expected long-term production losses to continue for some time.
The US Department of Agriculture (USDA) said dairy producers discarded an estimated $3m worth of milk due to lost electricity on farms and at dairy processing plants as a result of Hurricane Katrina.
A preliminary assessment of agricultural production losses due to Hurricane Katrina set a total of nearly $900m.
The problem for many dairy producers now is when they are likely to see USDA emergency aid coming through.
The DFA said the agriculture department was still processing applications for its 2004 Dairy Disaster Payment Program until 9 September this year. This scheme provided up to $10m to help dairy producers recover from hurricanes in Florida, Georgia and the east coast.
"The immediate need for financial assistance for the dairy farmer community hurt by Katrina is extremely critical. They need financial help soon so that rebuilding can get underway and further losses can be mitigated," said Hahn.