The new head of the New York Times’ editorial department decided several years ago to withhold a story about a secret government surveillance operation after meeting with government officials.

Dean Baquet, who became executive editor of the New York Times earlier this week, oversaw editorial operations at the Los Angeles Times in 2007 when a former AT&T employee brought information to one of his reporters that purported to expose the telephone company’s secret cooperation with the National Security Agency on a dragnet spy program that collected the phone calls of millions of American citizens.

The whistleblower, Mark Klein, is said to have worked with reporter Joseph Menn for two months on the report before the decision was made that the paper would not run the story. Klein told ABC News he was informed the decision not to pursue the story was made after Los Angeles Times editors met with government officials, including then-NSA head Gen. Michael Hayden.

Baquet told ABC News that the paper’s editors did, in fact, meet with government officials, but that the meeting had little effect on his decision to spike the report. Instead, Baquet said editors decided not to pursue the story because the documents Klein provided were too technical and the paper “could not figure out what was going on.”

Baquet said Menn “disagreed” and “was very disappointed” that the paper decided not to publish the report. The information was eventually made public when Klein agreed to be a witness in the Electronic Frontier Foundation’s class action lawsuit against AT&T. Menn, who now works at Thomson Reuters covering technologically-complex stories, declined to comment to The Desk when reached on Friday.

Baquet’s decision to spike the NSA story several years ago has drawn renewed criticism with his recent appointment as executive editor of the New York Times, a newspaper that famously delayed its scoop about the Bush administration’s use of warrantless wiretapping programs until well after Bush had been re-elected.

New York Times reporters James Risen and Eric Lichtblau were approached by a whistleblower in 2004 about secret NSA programs that collected e-mail and telephone data of millions around the world, including Americans. The whistleblower, later identified in a Newsweek article as Department of Justice attorney Thomas Tamm, was concerned that the new NSA surveillance program violated privacy laws and skirted Fourth Amendment protections.

Editors at the New York Times decided to withhold the story after government officials told the paper that disclosing the secret program would endanger the lives of American citizens. However, the paper finally published the report in late 2005 after editors learned that Risen had started writing a book that would have disclosed the program anyway.

The decision to withhold the story drew immediate comment and criticism from journalists, privacy advocates, government officials and New York Times readers. Whistleblowers snubbed the New York Times and began began leaking information on NSA programs to other publications, including USA Today and the Baltimore Sun.

One such whistleblower, former government contractor Edward Snowden, settled on Guardian journalist Glenn Greenwald for what would be the largest disclosure of classified intelligence information in U.S. history. His decision to pick the Guardian reporter was based in part on the New York Times’ decision to withhold their NSA scoop for 18 months, Greenwald wrote in his new book No Place to Hide.

“Snowden had been clear from our first conversation about his rational for distrusting the establishment media with his story, repeatedly referring to the New York Times’ concealment of NSA eavesdropping,” Greenwald wrote. “He had come to believe that the paper’s concealment of that information may very well have changed the outcome of the 2004 election.”

Bill Keller, then the executive editor of the New York Times, wrote in a 2006 response to a reader letter than the Times’ decision to delay the report was to give Risen and Lichtblau more time to research the programs after the government made “compelling” arguments “that publishing what we then knew would compromise ongoing anti-terror operations, and they challenged our reporting on the issue of whether the eavesdropping program was subject to serious oversight by the courts or Congress.”

Many believed things would change when Jill Abramson replaced Keller in June 2011. But now some are concerned that the paper will once again assume a cozy relationship with the government under Baquet, who replaced Abramson earlier this week.

“Jill Abramson was probably the best advocate for an adversarial relationship between the government and the media,” Greenwald said, noting Abramson’s attempt to hire the Guardian editor who oversaw Greenwald’s reporting on the NSA documents.

“Her successor, Dean Baquet, does have a really disturbing history of practicing this form of journalism that is incredibly subservient to the American national security scene,” Greenwald said, “and if his past record and his past actions and statements are anything to go by, I think it signals that the New York Times is going to continue to descend downward into the sort of journalism that is very neutered and far too close to the very political factions that it is supposed to exercise oversight over.”