Microsoft may be getting preferential treatment from the Bush administration’s Department of Justice because one of the department’s key lawyers was a top antitrust lawyer for the firm that represented Microsoft in the lengthy antitrust suit a few years ago.

So reports the New York Times. The newspaper reports that the department’s top antitrust official, Thomas O. Barnett, “had until 2004 been a top antitrust partner at the law firm that has represented Microsoft in several antitrust disputes.”

Barnett recently took an exceedingly controversial move in his official position regarding an antitrust complaint filed against Microsoft by Google. Not only did he dismiss Google’s claims in a memo, but he sent the memo to attorneys general around the country, and an attempt to dissuade them from pursuing Google’s claims.

The Times notes that this is extremely uncommon, and that previous to this memo, the attorneys general “could not recall receiving a request by any head of the Justice Department’s antitrust division to drop any inquiry.”

Whatever you think of the merits of Google’s antitrust claims, Barnett’s actions have the smell of a conflict of interest.

Barnett, though, seems to have shot himself in the foot. Attorneys general were so outraged by the memo that “Prosecutors from several states said they intended to pursue the Google accusations with or without the federal government.”

I’ll talk about the actual Google complaint in a future column. But Barnett shouldn’t be involved in this action one way or another, and ironically, he may end up hurting Microsoft more than he helped them with the heavy-handed way he tried to squash the complaint.