The Justice Department official acting as solicitor general on the sensitive case of tax exemptions for segregated private schools has taken the unusual step of disassociating himself from a key part of the government's legal argument to the Supreme Court.

Lawrence G. Wallace, a 14-year veteran of the department, signed the brief in the case involving Bob Jones University of Greenville, S.C., and Goldsboro (N.C.) Christian Schools. But he said in a footnote on the first page that he didn't agree with the new government position on the law in the case.

The Reagan administration, in a reversal of a long-standing policy, contends that the Internal Revenue Service doesn't have the authority to deny tax exemptions to discriminatory schools. The brief noted that Wallace had defended the IRS authority in the department's filing at the court in September, before last month's policy reversal, and also prepared a draft brief in January making the same arguments.

The footnote said Wallace "fully subscribes" only to the government's position on the second legal issue in the case--that First Amendment religious protections don't by themselves prevent the IRS from denying exemptions.

Wallace is acting on the case because Solicitor General Rex E. Lee excused himself. Legal authorities said Wallace's move was quite unusual, and some thought it was a sign of discomfort in the supposedly autonomous solicitor general's office.

Erwin N. Griswold, who was solicitor general from 1967 to 1973, during the Johnson and Nixon administrations, said in a telephone interview yesterday that he viewed Wallace's actions "as an attempt to preserve the credibility of the office."

Griswold said he doubted that the Supreme Court would pay much attention to the Justice Department's position in the case because "it has so obviously flip-flopped and so obviously influenced by politics."

He added that he refused to sign a brief once on a draft issue case during the Nixon administration because he felt the government's position was "bad policy and bad law." The Supreme Court rejected the government position without dissent, Griswold recalled.

Lee said he didn't feel the government's actions on the Bob Jones case raised questions about his office's credibility, which he called "the principal asset of this office."

"I think they the justices will recognize that from time to time things will be done a little differently," he said.

The Reagan administration asked the Supreme Court to dismiss the case as moot in January, when it announced it was reversing the policy denying exemptions.

Last week, however, an appeals court blocked the exemptions. So Thursday the government said the case should be argued after all.