Government lawyers said on Wednesday they would not appeal a decision by a Michigan federal judge who dismissed charges involving FGM as unconstitutional, ruling it was a state issue.
Congress in 1996 outlawed FGM, a ritual that involves partial or total removal of external genitalia, which the World Health Organization has called "a grave violation of the human rights of girls and women."
Half a million girls and women in the United States have undergone or are at risk of undergoing FGM, according to the U.S. Centers for Disease Control and Prevention.
The decision by the U.S. government "is sending a damaging message to law enforcement, the courts and to the courageous survivors who are breaking the silence around FGM," said Shelby Quast, an office director for Equality Now, an international human rights organization, in a statement.
About half of the nation's 50 states have laws outlawing the practice. Michigan law forbids the practice, but its law took effect after the case in question.
In the Michigan case, a federal judge late last year dismissed FGM charges against a doctor and others from the local Indian Dawoodi Bohra community involved in the mutilation of nine young girls in Detroit.
The judge said lawyers failed to prove that the federal government had the authority to regulate FGM and that such power lay in the hands of the states.
This week, Solicitor General Noel Francisco wrote in a letter to Congress that the Department of Justice "reluctantly determined" the wording of the law fails to defend the government's authority to enforce it.
He called FGM a "heinous practice" that "should be universally condemned" and urged Congress to fix the law.
Quast took issue with the solicitor general's reason, saying that girls are taken across state lines or outside the country for FGM, making it a federal issue.
Two months ago, the Department of Justice issued a statement on the International Day of Zero Tolerance for Female Genital Mutilation, calling it a federal crime punishable by imprisonment or removal from the country.
In a tweet on Thursday, former U.S. Secretary of State Hillary Clinton said it was the government's responsibility to defend against FGM.
"They're choosing instead to abandon the fight for the health and human rights of women and girls around the world," she wrote on Twitter.
A criminal case against the Michigan doctor and others will continue based on other charges, including conspiracy and obstruction of justice, experts said.