Lanny Breuer, the assistant attorney general in charge of the department's criminal division, said the U.S. request that Polanski be sent to the United States was completely supported by treaty, facts and the law.
The underlying conduct in the criminal case against Polanski "is, of course, very serious" and the department is "deeply disappointed" by the Swiss rejection, Breuer told reporters at a news briefing on a separate topic.
The U.S. government will review its options, Breuer added, but declined to discuss them.
At the State Department, spokesman P.J. Crowley said: "The rape of a 13-year-old girl by an adult who should know better and does know better is a crime. And we will continue to seek justice in this case."
The United States has been seeking Polanski's return to be sentenced for having sex in 1977 with a 13-year-old girl.
On Monday, Polanski was declared a free man after Switzerland said the U.S. had failed to address arguments by Polanski's lawyers that the 76-year-old filmmaker had actually served his sentence before fleeing Los Angeles three decades ago.
Polanski's lawyers have said the now-deceased judge in the case intended to treat a 90-day diagnostic study in prison as Polanski's entire punishment.
In May, a judge in California denied Polanski's request to unseal testimony about the sentencing procedure by the former prosecutor in the case, Roger Gunson. Los Angeles Superior Court Judge Peter Espinoza said he was satisfied that the Swiss had the information they needed.
Based on references to Gunson's Jan. 26 testimony in U.S. courts, the Swiss said it "should prove" that Polanski served his sentence after undergoing a diagnostic study.