President Reagan's decision to grant tax exemptions to private schools that discriminate against blacks was not just an act of administrative discretion but violates the law, the Lawyers Committee for Civil Rights Under Law charged yesterday in seeking an injunction that could lead to a constitutional confrontation between the executive and judicial branches.

Reagan portrayed the old policy of denying exemptions as an example of "administrative fiat," suggesting the executive branch had gone beyond its authority in the denials. But the civil rights group said he is challenging a federal court decision later affirmed by the Supreme Court, not an arbitrary policy decision by a federal agency.

The administration is aware of this court decision, but is interpreting it narrowly. Its interpretation is that it applies to only one state, Mississippi. But even that limited view of the court case has produced a bizarre effect that Treasury and Justice Department officials neglected to mention when they made their action public. Under Reagan's proposal, there will still remain one state--Mississippi--where segregated private schools cannot receive tax exemptions.

The Reagan plan to permit such tax exemptions cannot be extended to Mississippi, government lawyers said, without placing the Internal Revenue Service and its parent, the Treasury Department, in contempt of the 1971 injunction by the U.S. Circuit Court of Appeals here.

To avoid being in contempt, the government plans to begin issuance of tax exemptions in states other than Mississippi and perhaps later ask a court to dissolve the 1971 injunction, which was upheld by the Supreme Court.

The Lawyers Committee for Civil Rights Under Law, which argues that the 1971 decision was not limited to Mississippi and therefore is being violated by Reagan, filed papers in U.S. District Court yesterday seeking to head off the Reagan administration action.

In 1971, Judge Harold Leventhal of the D.C. Circuit Court of Appeals foresaw that the issue might become controversial and sought to head off confusion when he issued the injunction.

"To obviate any possible confusion the court is not to be misunderstood as laying down a special rule for schools located in Mississippi. The underlying principle is broader, and is applicable to schools outside Mississippi," he wrote.

Leventhal, now dead, also saw that future administrations might attempt to grant tax exemptions and sought to frustrate them.

The IRS had thrown in the towel and asked him not to issue a permanent injunction because it was willing voluntarily to halt granting tax exemptions to the avowedly segregationist schools, many of which had sprung up in response to desegregation of public schools.

Leventhal wrote that the black children and parents of Mississippi, on whose behalf the injunction was requested, "are entitled to a declaration of relief on an enduring, permanent basis, not on a basis that could be withdrawn with a shift in the tides of administration." So he went ahead and issued his order finding that the Internal Revenue Code of 1954 requires denying tax exemptions to schools practicing racial discrimination.

He based this decision on an established legal definition of a charity and found that there was a strong legal tradition that no organization can be a charity that is engaged in an illegal activity.

William Bradford Reynolds, the assistant attorney general in charge of the civil rights division, echoed the argument Reagan has used in an interview with United Press International yesterday.

He made no mention of the appellate or Supreme Court rulings on tax exemptions, but said the subsidies were denied for "essentially political reasons."

Reynolds, as Reagan did in a statement Tuesday, denied any racist intent. "I think that it was absolutely not a racist policy at all," he said. Ignoring the fact that the courts, including the Supreme Court, have ruled on the issue, Reynolds said it is "terribly crucial" that Congress, not the executive branch, deal with questions such as tax relief for segregated private schools.

Reagan, who also has made no mention of the judicial decisions on the issue, said Tuesday that "the sole basis" of his administration's decision was to prevent agencies such as the IRS from governing "by administrative fiat."

Reagan's statement Tuesday that he would submit legislation to deny tax exemptions to segregated schools was denounced by civil rights groups. NAACP executive director Benjamin Hooks said: "I don't think it's even a half-hearted move. It's silly to me. It's Orwellian double-talk, double-speak."

In the time before Congress acts on legislation, the IRS will be granting tax exemptions, according to the Reagan administration plan. Treasury officials said more than 100 private academies have been denied tax exemptions on the grounds that they practice racial discrimination.