WASHINGTON -- The special prosecutor in the Iran-contra affair said yesterday that he will ask the Supreme Court to reinstate the criminal conviction of former National Security Adviser John M. Poindexter.

Independent Counsel Lawrence E. Walsh, who had not made up his mind earlier, told the U.S. Circuit Court of Appeals here that he was taking the case on to the Supreme Court to try to salvage the five guilty verdicts against Mr. Poindexter.

The former White House aide to ex-President Ronald Reagan had been convicted of a plot to disrupt Congress' probe of the Iran-contra scandal by destroying documents, of obstructing that inquiry and of lying to Congress. His six-month jail sentence, which he had not served, was overturned along with the verdicts. Mr. Walsh's appeal to the Supreme Court will be an attempt to revive a major conviction in a case growing out of the scandal that nearly brought down Mr. Reagan's presidency.

The other major case, against Poindexter aide Oliver L. North, ended after Mr. North's convictions were overturned by the Circuit Court, and the Supreme Court turned aside an appeal by Mr. Walsh in that case.