Clemon told Holder in a recent letter that the case brought by federal prosecutors in Birmingham against Siegelman was the "most unfounded criminal case" he ever presided over.
The judge said he did not have personal knowledge of the circumstances surrounding Siegelman's prosecution and conviction in a government corruption case in Montgomery. But Clemon was critical of the earlier attempt to prosecute Siegelman in a mail fraud case. Prosecutors dropped the case after Clemon told them there was no basis for a conspiracy charge.
U.S. Attorney Alice Martin of Birmingham said she disagreed with Clemon and called his comments inappropriate "seeing that he was the judge."
The Associated Press on Thursday obtained a copy of the letter dated May 13. Clemon based his request for an investigation of the Montgomery prosecution on the earlier case that was presented in his court.
"Given my experience with his unwarranted prosecution in the Northern District, and in the interest of ensuring that Justice Department cases are handled fairly and consistent with its commitment to justice, I strongly support a thorough investigation by your office of allegations of prosecutorial misconduct in Mr. Siegelman's prosecution in the Middle District," Clemon wrote.
Clemon did not immediately return a call Thursday seeking comment about the letter.
Siegelman and former HealthSouth CEO Richard Scrushy were convicted in 2006 in a government corruption case in Montgomery. Prosecutors said Siegelman appointed Scrushy to a key hospital regulatory board in exchange for Scrushy arranging $500,000 in contributions to Siegelman's campaign for a lottery.
Siegelman was sentenced to more than seven years in federal prison and is currently free on bond while his conviction is appealed. Scrushy is serving an almost seven year federal prison sentence.
Siegelman, a Democrat, has claimed that his prosecution was politically motivated and was initiated by the administration of former Republican President George Bush. Siegelman's attorneys and supporters have been urging President Barack Obama's administration and Holder, the new Attorney General, to investigate the prosecution of the former governor.
Vince Kilborn, Siegelman's chief attorney, said Thursday he hopes the letter from Clemon will make a difference.
"It's a letter from a well respected federal judge based on his eyewitness observations of a government prosecution of Governor Siegelman," Kilborn said.
Clemon was Alabama's first black federal judge and served almost 30 years on the federal bench.