A Tyson Foods Inc. (TSN) unit has agreed to pay $2 million in civil penalties to settle allegations that it failed to properly operate a waste treatment system at a Nebraska meat-processing facility, the Justice Department announced.

The department alleged that the waste treatment lapses took place at a Tyson Fresh Meats facility in Dakota City, Neb., and resulted in toxic discharges into the Missouri River.

Authorities said the Tyson facility violated a federal pollution-discharge permit and a 2002 consent decree that required the facility to improve its waste treatment.

The violations took place from July 2003 through March 2004, the department said.

Tyson spokesman Gary Mickelson said the company cooperated with state and federal regulators and made operational and equipment changes when it became aware of the wastewater issues.

"Those issues have been resolved and the plant's Dakota City wastewater treatment system is operating effectively," he said.

-By Brent Kendall, Dow Jones Newswires; 202-862-9222; brent.kendall@dowjones.com