The operator of the nation's largest landfill has agreed to pay a $600,000 penalty for illegally storing PCB compounds, the Environmental Protection Agency announced yesterday.

The operator, Chemical Waste Management Inc. of Oak Brook, Ill., also has agreed to remove the compounds and burn them in EPA-approved incinerators by the end of 1985, the agency said.

PCBs, or polychlorinated biphyenyls, are often contaminated with dioxins, one of the most powerful toxins known. PCBs are chemically inert and extremely long-lasting.

The firm stored PCBs at Emelle, Ala., about 75 miles west of Mobile, in anticipation of burning them at sea. But it has been unable to win EPA permits to operate its incineration ships.

Since the deadline of Dec. 31, 1983, for removing the material from Emelle, 2.8 million gallons have been in eight large tanks at the landfill illegally, EPA said.

The company has agreed to analyze the tanks for dioxins, conduct a comprehensive groundwater and geological study of the landfill site, step up environmental monitoring and auditing and report extensively on its future handling of PCBs, the agency said.

The auditing of site practices by an independent consultant has never been incorporated in previous consent decrees, EPA said.

Hugh Kaufman, an EPA toxic substances official often critical of his agency's actions, said the firm has earned $3 million to $5 million it was paid for destroying the PCBs. "If they're not fined equal to the amount they made by their illegal action, you're promoting illegal action," Kaufman said.