Journalism in the Trump era has featured a staggering number of leaks from sources across the federal government, providing bombshell revelations about everything from clandestine meetings with Russian officials to petty infighting at the White House.

But the arrest of Reality Leigh Winner, an intelligence contractor accused of leaking a classified report about Russian meddling in the 2016 election, has raised concerns about the measures taken by news organizations to protect confidential informers, with some reporters worrying about a chilling effect on potential sources.

Veteran journalists did not hold back on Tuesday in criticizing The Intercept, the online news outlet that published an intelligence report from the National Security Agency. About an hour after the report’s publication on Monday, the Justice Department said it had charged Ms. Winner, 25, with violating the Espionage Act, saying she had leaked the report.

The Intercept said it did not know the identity of its source, who mailed the document in a plain envelope. But an F.B.I. affidavit released on Monday described a series of actions by the news outlet, such as sharing a copy of the document with the National Security Agency, that allowed the document’s provenance to be quickly deduced.