ANNE BURFORD has always argued that Congress took the wrong scalp in the furor over the Environmental Protection Agency in 1982 and 1983. The former EPA administrator says the villain was the Justice Department. Last December the House Judiciary Committee, all but two of its Republicans dissenting, also concluded that Justice bent the EPA controversy out of shape. Among other things, the committee asserted in an extraordinary report of more than 3,000 pages that during the controversy several senior Justice Department and White House officials lied.

The committee asked Attorney General Edwin Meese to seek appointment of an independent counsel to investigate. He is now reported to have done so. The law providing for such investigations has been criticized in the past for magnifying frivolous charges. Here it is useful. These are serious charges and need to be authoritatively met.

The EPA affair had to do mainly with the Superfund program to clean up leaking industrial dumps before they poison the water supply. The program was new when the Reagan administration came to office and, to a large extent, fell to Mrs. Burford to shape. Critics complained that she did so with the back of her hand -- that the administration was indifferent to the problem, slow to take action, reluctant to spend the money that Congress had authorized and too cozy with industry in setting clean-up terms. The agency was accused of making sweetheart deals with polluters. It was also accused of timing enforcement decisions for partisan political reasons. The issue was good politics in that election year as well as a fair target on substantive grounds; at one point there were five House subcommittees investigating EPA.

Many people think in retrospect that the agency could have weathered the storm had officials not made the classic mistake of responding in part by seeking to cover up. The only one convicted of a crime in the whole episode was assistant EPA administrator Rita Lavelle, for lying. And the final issue in the long imbroglio was not environmental enforcement but executive privilege. It was here that the Justice Department played its major role. Justice officials prevailed on the White House, Mrs. Burford objecting, to invoke privilege and deny some documents to Congress. The House then cited Mrs. Burford for contempt; the contempt citation helped force her resignation.

The committee says that Justice had no basis for invoking privilege; that Justice officials "misrepresented key facts in the controversy to the president"; that Justice and White House officials made several false certifications to Congress; that Justice officials "filed false and misleading documents" with a federal district court; that officials discussed opening a criminal investigation of Miss Lavelle as a cover for denying information to Congress; that officials later also tried to obstruct the Judiciary Committee's investigation.

The named officials have taken sharp issue with the committee report. We hope the independent counsel will be given the widest possible latitude to sift among the varying accounts. We hold no brief for Mrs. Burford's record as head of EPA. But the Judiciary Committee has raised uglier issues.