WASHINGTON—Supreme Court justices on Wednesday sharply challenged the Justice Department’s lawyer in an immigration case, saying the government’s position risked stripping citizenship from naturalized Americans over minor infractions for which they were never charged.

In a case involving a Bosnian Serb immigrant who lied to immigration officials, Justice Department lawyer Robert Parker told the court that any lie on the naturalization form—even involving such inconsequential facts as a former nickname or once driving over...