AUGUSTA, Ga. — It was a farm idea with a big payoff and supposedly no downside: ridding lakes and rivers of raw sewage and industrial pollution by converting it all into a nutrient-rich fertilizer.

Then last week, a federal judge ordered the Agriculture Department to compensate a farmer whose land was poisoned by sludge from the waste treatment plant here. His cows had died by the hundreds.

The Associated Press also has learned that some of the same contaminants showed up in milk that regulators allowed a neighboring dairy farmer to market, even after some officials said they were warned about it.

In one case, according to test results provided to the AP, the level of thallium — an element once used as rat poison — found in the milk was 120 times the concentration allowed in drinking water by the Environmental Protection Agency.

The contaminated milk and the recent ruling by U.S. District Judge Anthony Alaimo raise new doubts about a 30-year government policy that encourages farmers to spread millions of tons of sewage sludge over thousands of acres each year as an alternative to commercial fertilizers. The program is still in effect.

Judge Alaimo ordered the government to compensate dairy farmer Andy McElmurray because 1,730 acres he wanted to plant in corn and cotton to feed his herd was poisoned. The sludge contained levels of arsenic, toxic heavy metals, and PCBs two to 2,500 times federal health standards.

Also, data endorsed by Agriculture and EPA officials about toxic heavy metals found in the free sludge provided by Augusta’s sewage treatment plant was “unreliable, incomplete, and in some cases, fudged,” Judge Alaimo wrote.