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Separately, a top ATF official has been reviewing Mr. Dodson’s manuscript for any concerns about sensitive or classified information, potentially leaving open the possibility a process by which it could be published for free, a senior law enforcement official told The Times.

The gun-walking strategy — part of an undercover case called Fast and Furious — violated ATF’s long-standing policy to interdict weapons from straw buyers.

In all, ATF officials permitted more than 1,700 semi-automatic weapons to flow through the hands of straw buyers for the Mexican cartels, with many crossing the border.

Senior ATF officials hoped to trace the guns to crimes, then make a bigger case against the Mexican drug lords. The strategy, however, backfired when hundreds of the weapons began showing up at crime scenes on both sides of the border, including at the December 2010 murder of U.S. Border Patrol Agent Brian Terry.

The Justice Department initially denied guns knowingly had been allowed to flow across the border, then months later reversed course and admitted the tactic had been used for more than a year. The change in story led to allegations of a cover-up.

The revelations exploded into public in spring 2011, catapulting Mr. Dodson and other ATF field agents who had objected into dual investigations by Congress and the Justice Department inspector general.

President Obama and Attorney General Eric H. Holder Jr. both claimed they knew nothing about the strategy until the controversy erupted, but the president has invoked executive privilege to block Congress from seeing certain documents, thus thwarting the completion of that probe. A court recently ruled in favor of Congress in the ongoing legal dispute.

Both the congressional and inspector general investigations concluded that the gun-walking tactics were poorly conceived and put lives in jeopardy. The fallout forced the ouster of numerous top officials, including the U.S. attorney in Phoenix, Dennis Burke, and the acting director of the ATF, Kenneth Melson.

The ATF, under new director B. Todd Jones, says it has imposed sweeping procedures to ensure gun-walking doesn’t occur in future cases.

The book dispute with Mr. Dodson, however, is not the first First Amendment controversy to erupt in the aftermath of the scandal.

Last year, Mr. Jones raised alarm in Congress and inside his own agency when he released a videotaped message that warned agencies that there would be “consequences” if agents blew the whistle on wrongdoing outside their chain of command.

The message led to claims that whistleblowing would be chilled, and ATF subsequently clarified Mr. Jones’ remarks to emphasize that the agency would not interfere with legitimate whistleblowing activities.