Former Environmental Protection Agency official Rita M. Lavelle was indicted yesterday on charges of perjury and obstructing a congressional investigation by allegedly lying about her role in a toxic waste case involving her former employer.

Lavelle was accused of secretly warning the firm, 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.

Lavelle, 35, managed the EPA's $1.6 billion "Superfund" program to clean up toxic waste dumps until she was fired Feb. 7 by President Reagan. Her dismissal triggered the investigations that led to the departure of more than a dozen top agency officials, including former administrator Anne M. Burford.

The five-count indictment returned by a federal grand jury here said Lavelle also lied to Congress last winter when she denied awarding or delaying toxic waste cleanup grants based on political considerations during the 1982 campaign. The indictment said Lavelle had used an "election track" in handing out grants "in order to assist candidates for public office in 1982."

Lavelle, who was acquitted July 22 on contempt of Congress charges after refusing to honor a House subpoena, faces a maximum of 25 years in prison and $21,000 in fines if convicted.

The criminal charges are the first to arise from specific allegations of mismanagement, conflict of interest and "sweetheart" deals with industry that rocked the EPA earlier this year.

Law enforcement sources said yesterday that the six-month FBI investigation is nearing an end and that it was unlikely to result in indictments against other subjects of the probe, including former acting administrator John W. Hernandez Jr., former general counsel Robert M. Perry and former agency consultant James W. Sanderson. Justice Department spokesman John Russell said the department will issue a status report on the investigation next week.

Lavelle's attorney, James J. Bierbower, said he had not seen the indictment, but that "apparently they've got someone who says something different" than Lavelle's testimony. "It comes down to the old line: What did you know and when did you know it?"

The perjury counts involve Lavelle's testimony before a House Public Works and Transportation subcommittee chaired by Rep. Elliott H. Levitas (D-Ga.) and the Senate Environment and Public Works Committee, as well as a written statement to a second House subcommittee.

Each time, Lavelle said she did not learn that Aerojet-General had disposed of wastes at the Stringfellow site near Riverside, Calif., until June 17, 1982. The following day, Lavelle formally disqualified herself from EPA decision-making in the case.

"I found out June 17 for the first time that Aerojet was one of the many companies who had dumped at this site . . . ," Lavelle told the Senate committee last February.

Aerojet was on a list of companies facing possible prosecution for failing to clean up the wastes they deposited at Stringfellow. Justice later filed suit to force such a cleanup, but Aerojet was not named because of its minor role.

The indictment said Lavelle was warned about Aerojet's role in the case at a May 28, 1982 staff meeting, as some EPA officials previously alleged. This was about three weeks before she testified she first learned of the Aerojet involvement. Lavelle "knew and believed" that her testimony "was false," the indictment said.

Instead, the indictment charged, soon after the May meeting Lavelle called John C. Andreason, general counsel and vice president of Aerojet-General, and disclosed that EPA officials had identified the company as a past user of the Stringfellow site. The indictment said Lavelle also continued to participate in the Stringfellow matter.

Tom Sprague, a spokesman for Aerojet-General, said the company "is certain the relationship between Aerojet, the EPA and Miss Lavelle has been ethical, honest and aboveboard at all times."

Lavelle perjured herself on the same issue in a statement she submitted last December to a House Energy and Commerce subcommittee headed by John D. Dingell (D-Mich.), the indictment charges. It said she also obstructed Dingell's investigation by making the allegedly false statements.

The indictment also rekindled last winter's controversy over whether the Reagan administration politically manipulated the Superfund program, charging that Lavelle lied when she testified that she "never participated" in such efforts.

"Lavelle participated in activity such as placing cleanup of certain sites on an 'election track' and delaying or hastening cleanup of certain sites with political considerations in mind," the indictment said, "and gave consideration to who's whom and who's representing what district . . . ."

The indictment said Lavelle ordered action on a hazardous waste site in Seymour, Ind., to assist the reelection campaign of Sen. Richard G. Lugar (R-Ind.). Lugar had been pressing for the $7.7-million grant, which was announced shortly before the election and was criticized for allowing corporate polluters to avoid millions of dollars in liability.

Lavelle was acquitted of failing to testify before the Dingell subcommittee after she told the jury she was depressed and too ill to testify.

"The jury had sympathy for her when she didn't show up," said House counsel Stanley Brand. "Maybe the jury will have less sympathy if they determine that when she did show up, she lied."