The federal government is polluting the nation’s waterways at a record rate, violating the Clean Water Act six times as often as it did in 1993, and at a higher rate than private companies, according to a new report by the EPA. Nearly four of every 10 federal facilities, primarily those operated by the Defense and Energy departments, were in significant violation of the act in 1998. In comparison, three of every 10 private facilities violated the law during the same year. Federal agencies are exempt from many of the penalties levied against private companies under the Clean Water Act. A separate report released yesterday by the U.S. Public Interest Research Group says the EPA has not done enough to deter government agencies or businesses from polluting waterways.