Former Environmental Protection Agency official Rita M. Lavelle yesterday pleaded not guilty in federal court to charges that she lied to a congressional subcommittee about her role in a toxic waste case involving her former employer.

Lavelle was indicted Aug. 4 on charges of perjury and obstructing a congressional investigation into her management of the EPA's $1.6 billion "Superfund" for cleaning up hazardous waste.

Specifically, she is accused of secretly warning Aerojet-General Corp. that it was a potential target of a government lawsuit during a period when, she later insisted under oath, she had no idea the firm had disposed of hazardous wastes in the Stringfellow Acid Pits in California.

The indictment also charges Lavelle with lying to Congress last winter when she denied awarding or delaying toxic waste cleanup grants based on political considerations during the 1982 campaign.

Lavelle, 35, last month was found not guilty by a federal jury on a charge of contempt of Congress resulting from her failure to testify before a House subcomittee investigating alleged mismanagement of the cleanup fund.

She appeared briefly yesterday in U.S. District Court before Judge Norma Holloway Johnson, who released Lavelle on her personal recognizance pending a status hearing in the case Aug. 25.

On Thursday the Justice Department announced that it would not file criminal charges against six other former EPA officials after a six-month probe of agency activities.