Alarmed by research linking chemicals used to make Scotchgard and Teflon to cancer, liver disease and other health problems, the federal government spent the last decade pressuring manufacturers to phase out the stain-resistant compounds.

But scientists at the U.S. Environmental Protection Agency recently discovered that a different industry – metal plating – is dumping high levels of the chemicals into sewers in Chicago and Cleveland, and likely is doing the same thing in scores of other cities.

The finding is worrisome because the chemicals, known as perfluorinated compounds, or PFCs, wash unfiltered through sewage treatment plants into lakes and streams. The chemicals don’t break down in the environment, and traces are showing up in the blood of people and wildlife around the globe.

At one Chicago-area metal plating shop, which the EPA does not name, the agency found PFCs being flushed into the sewers at concentrations of 12,214 parts per trillion, far higher than the 2.5 parts per trillion found in water piped into the factory.

Levels were even higher at one of the Cleveland shops: more than 54,000 parts per trillion.

Mindful that those amounts are some of the highest detected in wastewater to date, career staff at the EPA are urging the Obama administration to crack down on the metal plating industry’s use of PFCs, which are used to suppress fumes during the plating of chrome automotive bumpers, wheels and other parts.

In 2007, records show, the Bush administration created a special exemption that allowed metal plating shops to avoid any regulations on perfluorinated compounds because the industry said it had no alternatives. Agency leaders in Washington granted the waiver despite objections from the EPA’s top official in Chicago, who noted in an internal memo that safer alternatives are readily available.

“We had plenty of warning signs,” said Mary Gade, the former EPA regional administrator, recalling the debate at the time within the agency. “Our point was these chemicals pose serious concerns for health and the environment.”

Muddying the issue is that PFCs have been considered a relatively inexpensive way for metal plating shops to curb emissions of another highly toxic substance, hexavalent chromium.

Industry representatives contend they need time to test PFC-free chemicals, though one of the nation’s largest metal platers already has switched to a solution that is significantly less toxic.