WASHINGTON—A federal judge blocked most of a White House executive order punishing Perkins Coie, saying the administration had put itself at odds with the First Amendment by targeting the law firm based on President Trump’s dislike of its work for his political opponents.

U.S. District Judge Beryl Howell in Washington, D.C., issued her decision in lengthy remarks at the end of a Wednesday hearing, excoriating the administration for an order that she said likely violated the Constitution on multiple fronts and threatened to undermine bedrock principles of the U.S. legal system, namely that even the unpopular or politically disfavored are entitled to protection and representation under the law.