Federated Farmers says a move by Watercare Services in Auckland to take more water from the Waikato River to cope with big population growth could put too much pressure on the river.
The agency is looking for new sources to avoid Auckland outgrowing its current supply within 35 years.
It already takes up to 27 percent of its supply from the Waikato River and one future option is to take up to a third more.
Federated Farmers Waikato provincial president James Houghton told Nine to Noon it fears the region is over-allocating water.
He said Watercare's application would exceed the water allocation from the river, which would leave nothing for future projects and opportunities in the Waikato region.
Watercare says it won't comment as it's too early in the consent process.