In a sharp rebuke of the Albany County district attorney, a state judge on Monday dismissed a criminal case against the operators of a pharmacy in Florida at the center of a national steroid scandal that implicated major sports figures.

The judge, Stephen Herrick of Albany County Court, noted in dismissing the case that the operators of the company, Signature Pharmacy, were pursuing a civil lawsuit against the district attorney, P. David Soares, in which they accused him and his office of committing federal civil rights violations stemming from the criminal case.

Judge Herrick said that in light of the civil lawsuit brought by the pharmacy’s operators, Mr. Soares and his office had a professional and financial stake in the outcome of the criminal case against the operators.

“In the present matter, the court has found a conflict of interest sufficient to warrant dismissal of the indictment,” the judge wrote in the six-page decision. “Likewise, the court finds that this demonstrated conflict of interest warrants the disqualification of the Albany County district attorney’s office from further prosecution of this matter.”

The district attorney’s office condemned the judge’s decision, saying it established a dangerous precedent that undermined the legal system.

“Judge Herrick’s decision is a get-out-of-jail-free card for every criminal defendant in New York State,” said Heather Orth, a spokeswoman for Mr. Soares. “His message to defendants is, ‘If your D.A. is being too tough on you, sue him, and you can get a new one.’ ”

Mr. Soares’s statewide profile has grown as a result of his investigations of top New York public officials, most recently on the question of whether to prosecute Gov. David A. Paterson on perjury charges.

The criminal case dismissed on Monday and the subsequent civil lawsuit centered on an investigation that Mr. Soares opened several years ago that resulted in a highly publicized raid on Signature Pharmacy in Orlando, Fla., which prosecutors had accused of being the supplier of at least $10 million of controlled substances sold to customers in New York.

The raid, in February 2007, led to the arrests of five people associated with Signature: Naomi and Robert Loomis, the couple that owns the pharmacy; Kenneth Michael Loomis, Mr. Loomis’s brother and a pharmacist at the company; and two former employees, Kirk Calvert and Tony Palladino.

Over the summer, a federal judge in Florida denied Mr. Soares’s motion to dismiss the civil suit, a fact noted in the ruling on Monday. The judge, Gregory A. Presnell, said Mr. Soares led a criminal case riddled with flaws, including arrests that potentially were illegal. The judge also accused Mr. Soares of taking steps to attract the maximum amount of attention from the media.

Judge Presnell also said he did not understand why Mr. Soares believed he had a legal basis to pursue the investigation, noting that Signature had no offices in New York and that the people charged had never set foot in the state.

In 2008, Judge Herrick threw out criminal indictments against the five Signature defendants, citing a series of blunders and missteps by Albany County prosecutors that he said had prejudiced the case. But Mr. Soares charged the five again over the summer.

Mr. Soares has said that Signature was at the center of a nationwide ring of shady Web sites and unethical doctors who had made steroids and other controlled substances easy to obtain over the Internet.

Prosecutors charged that the Web sites enabled doctors to provide prescriptions to numerous people, including professional baseball and football players seeking to improve performance, whom they had neither met nor diagnosed. Signature Pharmacy, prosecutors said, filled the prescriptions.

Mr. Soares has been at the center of several high-profile cases involving New York political figures in the last few years.

Most recently, Judith S. Kaye, the former chief judge of the State Court of Appeals, issued a report saying Governor Paterson misled state ethics regulators while testifying under oath about tickets he had obtained to a Yankees World Series game last year. But she left it to Mr. Soares to decide whether to pursue perjury charges against the governor; he has not yet made that decision.

Mr. Soares also led an investigation into the way former Gov. Eliot Spitzer’s administration handled the politically sensitive travel records of a Republican rival, Joseph L. Bruno during Mr. Bruno’s time as the Senate majority leader.

Mr. Soares drew criticism for his handling of that investigation after issuing conflicting assessments of the case and after interviewing Mr. Spitzer and other officials informally, rather than under oath. He ultimately filed no charges.

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