Factory-style farms that produce large amounts of waste will have to comply with a new water pollution rule the Bush administration is issuing to comply with a court-ordered deadline.

The new rule coming from the Environmental Protection Agency on Monday says all big concentrated animal feeding operations must apply for a permit to control pollution under the Clean Water Act, according to government sources and environmentalists familiar with the rule.

EPA Administrator Christie Whitman and Agriculture Secretary Ann Veneman were making the announcement.

EPA is requiring permit holders to develop a "nutrient management plan'' that sets limits on how much animal manure can be applied to fields. Animal manure typically contains nutrients such as nitrogen and phosphorus but also pathogens, salts and heavy metals like copper.

Years in the making, the rule deals with the concentrated manure from corporate agriculture that has led to fights between livestock farms and neighbors complaining about health and environmental effects.

The court-ordered deadline results from a broader settlement requiring EPA to update technology standards for industrial sources of water pollution. Runoff from agriculture is the biggest source of pollution in rivers, streams and lakes, the government says.

In 1992, EPA and the Natural Resources Defense Council, or NRDC, an environmental group, reached a court settlement requiring the agency to update its technology standards for several categories of industrial water pollution.

After study, EPA chose the factory-style farms as one of the industrial categories that needed improvement. Large-scale animal factories produce 220 billion gallons of manure annually, the government says.

The rule covers concentrated animal feeding operations, large and small. The new "duty to apply'' for a permit is aimed at the approximately 15,000 largest facilities with more than 1,000 "animal units'' — the actual numbers of specific animals vary depending on their type. These operations are generally concentrated on small land areas.

Melanie Shepherdson, an attorney with NRDC's clean water project, said the rule leaves too much discretion to states in regulating water pollution, and relies upon a system that is still largely voluntary.

Under existing law, concentrated animal feeding operations already are required to get permits because Congress 30 years ago said they must be regulated as sources of water pollution under the Clean Water Act's water pollution permitting program, she said.

But some operations are exempted from permitting, such as those that say they will discharge waste only during very severe storms.

"It's just that existing law isn't implemented,'' Shepherdson said. "Basically, the new rule is not going to fix this tremendous problem. In fact, it's just going to give factory farms the legal cover to continue polluting.''