WASHINGTON — The Justice Department told a lawmaker this week that it had stopped defending a federal prohibition on female genital mutilation because of flaws in the law, two weeks after it also began fighting the Affordable Care Act in court rather than defend it.

The department “reluctantly determined” that it could not appeal a federal judge’s decision to throw out a female circumcision case because the statute outlawing the practice needed to be rewritten, the solicitor general, Noel J. Francisco, wrote in a letter to Senator Dianne Feinstein of California, the top Democrat on the Senate Judiciary Committee.

The decision by law enforcement officials to step back from advocating two statutes is highly unusual. Defending laws on the books is a principal function of the Justice Department, and only about once a decade since World War II has it declined to support a law enacted by Congress, according to Walter E. Dellinger III, who served as the solicitor general during the Clinton administration.

While there are important differences between the two cases — Republicans have attacked the Affordable Care Act in the courts for years, while legal experts are debating whether the circumcision law is defensible — critics were troubled by what they fear is an emerging view inside the Justice Department that it is up to the Trump administration, not members of Congress, to decide whether a law has merit and should be enforced.