A Maricopa County Superior Court judge has disqualified County Attorney Andrew Thomas from an ongoing grand-jury criminal investigation into a $340 million county project because of a conflict of interest.

Presiding Criminal Court Judge Gary Donahoe removed Thomas from the case because the court-tower project under investigation by the grand jury is one that the County Attorney’s Office has provided legal advice on, according to court documents unsealed on Friday. Donahoe filed the ruling on Feb. 9.

Thomas has appealed the decision to the Arizona Court of Appeals.

Donahoe also denied requests from Thomas’ office to have an out-of-county judge rule on the matter and to remove from the case a private attorney retained by the county. The ruling also said that if Thomas wished to move the case forward, he would have to appoint a special prosecutor.

Thomas said the grand jury had met for a few months.

Grand juries are groups of citizens who review evidence and decide whether or not indictments should be issued. But grand jury matters are secret.

However, the Board of Supervisors and its legal team fought to get the records unsealed. The judge conceded Friday, saying that none of the reasons for secrecy applied because Sheriff Joe Arpaio’s office had already told the media an investigation on the court tower was under way.

“It strikes this court that any rationally thinking person would likely conclude that it appears improper for adversaries in a court proceeding to have the same lawyer,” Donahoe wrote.

But Thomas claimed that Donahoe was misinterpreting the law to the benefit of the court.

“The sheriff and I are very concerned by the decision because it ignores clear rulings from higher courts and suggests that the superior court can decide whether or not it’s above the law,” he said. “If there’s any conflict in this, is it not in a judge ruling that he should not be subject to criminal investigation as well as the other court officials?”

The judge’s ruling appears to agree with the board’s assertion that Thomas cannot investigate his own client - the board - after his office provided it legal advice. In the wake of a criminal investigation of Supervisor Don Stapley, the board essentially fired Thomas as its chief legal counsel and formed its own legal department, saying Thomas has too many conflicts.

“Thomas is saying to his clients: You can’t fire me,” said Wade Swanson, director of the board’s new civil-litigation office. “The judge says the same thing that the board’s been saying for weeks, if not months, which is that the board is entitled to obtain legal advice from lawyers who do not have a conflict of interest.”

Thomas also has filed a lawsuit against the creation of that litigation office.

Arizona Attorney General Terry Goddard agreed with Donahoe’s ruling.

“It’s black-letter law that conflicts of interest matter, especially for public prosecutors, both in the public perception and in the ability to do the job,” Goddard said. “And if there’s a conflict, you’ve got to step aside.”

He added, “You can’t use information that was gathered as part of your normal representation of a client in aid of a criminal prosecution.”

Goddard also is under investigation by Thomas and Arpaio’s offices for his handling of a prosecution of former state Treasurer David Peterson.

“The appearance is that they’re investigating everyone who disagrees with them,” Goddard said. “Is it just coincidental that he’s got a fight with the court on about 10 different items?”

The proposed court tower has been a bone of contention among county elected officials during the current financial crisis. The county is facing budget cuts and layoffs, but the board is spending $340 million to build a 16-story criminal court tower in downtown Phoenix, which officials say is needed to handle ever-increasing caseloads.

Arpaio and Thomas have both said the board should use the project’s money to float the county through tough times. The investigation involves the tower’s “funding and contracts,” according to a news release.

Arpaio, meanwhile, has submitted a records request asking for documents related to the project. On Dec. 12, Thomas served a grand-jury subpoena on Maricopa County officials seeking all records related to the court tower.

Thomas was particularly adamant about seeking information about the role of Tom Irvine in the court-tower project, including how much he has been paid and the circumstances of his hire. Irvine is the private attorney hired by the county.

“Those are the questions I’d like to ask him, and he won’t answer,” Thomas said.

Irvine is the attorney whose firm Thomas sought to have removed from the case.