A specially appointed attorney yesterday asked the Supreme Court to uphold the Internal Revenue Service's denial of tax exemptions to two racially discriminatory schools even though the Reagan administration renounced that authority in January.

The attorney, William T. Coleman Jr., secretary of transportation in the Ford administration and chairman of the NAACP Legal Defense Fund Inc., filed the brief in a case involving Bob Jones University of South Carolina and the Goldsboro Christian Schools of North Carolina. Coleman said that claims by the government that it still opposes racial discrimination are meaningless without such sanctions.

The administration's position now "is an empty assurance if schools that admittedly discriminate on the basis of race are nonetheless afforded significant tax benefits," Coleman argued. "Surely the constitutional and congressional command to eradicate the badges and incidents of slavery demand more."

The Supreme Court took the extraordinary step in April of appointing Coleman to defend the IRS after the Justice Department reversed its position on the case and said the service did not have statutory authority to deny the schools exemptions. Lower courts had upheld that authority.

The administration's action triggered a storm of protest. Its repercussions still are being felt, delaying Senate consideration of a tuition tax credit bill for parents with children in private schools.

Because the government now sides with the two discriminatory schools, the solicitor general's office has requested that time for oral arguments be divided between the schools, the Justice Department and Coleman. The Supreme Court has yet to approve the motion.

In his friend-of-the-court brief, Coleman called the IRS position an inevitable outgrowth of a longstanding policy that only organizations "charitable" in the common-law sense are entitled to tax exemptions.

He also argued that Congress has several times since 1970 upheld the IRS position, and he added that giving the schools exemptions would frustrate national policy opposing racial discrimination.

No date has been set for oral arguments in the case, but they could be scheduled for October, which would bring the issue into public view again just before the Nov. 2 elections. Some White House officials acknowledge that the administration's handling of the case has been a major political embarrassment.