The New York Times' recent report that the United States has been secretly helping Pakistan secure its nuclear arsenal contained another revelation. As with its 2005 expose of the Bush administration's illegal NSA domestic surveillance program, the Times sat on the Pakistan story at the request of the White House. Contrary to the repeated claims of President Bush and his amen corner, the New York Times has been more than deferential in letting the White House determine "all the news that's fit to print."
As the Times details, the Bush administration launched a $100 million program in the wake of the September 11 attacks to help the Musharraf government safeguard its nuclear weapons and material caches. That aid has included the shipment of sophisticated nuclear detection equipment, the training of Pakistani personnel in the United States and the construction of training facilities in Pakistan. After internal debate, the Bush administration decided against offering Islamabad American "permissive action links" (PAL) technology, used to "keep a weapon from detonating without proper codes and authorizations."
As it turns out, the New York Times held off on publishing the Pakistan nuclear security program for over three years:

The New York Times has known details of the secret program for more than three years, based on interviews with a range of American officials and nuclear experts, some of whom were concerned that Pakistan's arsenal remained vulnerable. The newspaper agreed to delay publication of the article after considering a request from the Bush administration, which argued that premature disclosure could hurt the effort to secure the weapons.

As the Politico details, the past statements of Pakistani officials, the current political instability in Pakistan and the withdrawal of the White House request led the New York Times to proceed with publication of the story now:

Gordon Johndroe, White House National Security Council spokesman, told the Politico that "it was determined in 2004 that publication of the information would be harmful."
But subsequently, Johndroe said, details of the secret program have "slowly, over time, become more public." For that reason, he added, "there was no point in still maintaining our objection to publication."
"We have to be very careful in choosing when to ask a media outlet not to run something," Johndroe said. "We have a responsibility not to hold them to an agreement when it is no longer necessary."

That was not the case, however, with the New York Times' December 2005 revelations regarding the NSA's clandestine program of domestic surveillance. Despite the almost certain illegality of President Bush's regime of domestic wiretapping without warrants, the Times withheld publication for over a year.
Nearly a dozen current and former officials, who were granted anonymity because of the classified nature of the program, discussed it with reporters for The New York Times because of their concerns about the operation's legality and oversight.
The White House asked The New York Times not to publish this article, arguing that it could jeopardize continuing investigations and alert would-be terrorists that they might be under scrutiny. After meeting with senior administration officials to hear their concerns, the newspaper delayed publication for a year to conduct additional reporting. Some information that administration officials argued could be useful to terrorists has been omitted.
Ironically, that delay was particularly fortuitous for George W. Bush. By sitting on the damaging story until after the 2004 election, the New York Times may have helped ensure Bush's return to the White House for four more years.
Of course, that did nothing to assuage the fury of President Bush, the Republican leadership and its echo chamber among the conservative chattering classes. On December 19th, 2005, President Bush raged about what he deemed "a shameful act" that is "helping the enemy". Claiming he didn't order an investigation, Bush added "the Justice Department, I presume, will proceed forward with a full investigation" At a subsequent press conference that same day, Alberto Gonzales suggested the inquiry - and retribution - that was to come. And as the controversy over the NSA program mounted, the President's right-wing allies called for the prosecution of Times' reporters James Risen and Eric Lichtblau.
The President and his defenders have short memories. After all, New York Times played an essential role in helping the White House sell the invasion of Iraq. Judith Miller and other Times' writers were indispensable in propagating the Bush administration's fraudulent claims concerning Iraqi weapons of mass destruction. It was no accident that Vice President Cheney in September 2002 referred to the paper of record as the definitive source on Iraq's acquisition of aluminum tubes for its nuclear program, misinformation the administration itself had provided the Times. For its part in enabling the war on Iraq, one would think the New York Times deserves conservatives' gratitude, not venom.
Back in 1962, James Reston of the New York Times honored President John F. Kennedy's urgent request to wait before publishing what he knew about Soviet missiles in Cuba. That respite let JFK address the nation on the Cuban missile crisis and formulate his blockade strategy that ultimately helped the United States defuse a potential nuclear showdown.
Now, with the Pakistan nuclear security story as with the NSA blockbuster, the New York Times has been more than deferential to the Bush White House in balancing national security concerns with the American people's right to know (especially about administration lawbreaking). As the Iraq fiasco shows, the Times if anything has been too compliant, its response too Pavlovian (if not that of a lap dog). The White House said sit and the paper sat. Bad dog. No biscuit.