"Future U.S. political leaders - those for whom the Cold War was not the formative experience that it was for me - may not consider the return on America's investment in NATO worth the cost," he told a European think tank on the final day of an 11-day overseas journey.
Gates has made no secret of his frustration with NATO bureaucracy and the huge restrictions many European governments placed on their military participation in the Afghanistan war. He ruffled NATO feathers early in his tenure with a direct challenge to contribute more front-line troops that yielded few contributions.
Even so, Gates' assessment Friday that NATO is falling down on its obligations and foisting too much of the hard work on the U.S. was unusually harsh and unvarnished. He said both of NATO's main military operations now -- Afghanistan and Libya -- point up weaknesses and failures within the alliance.
"The blunt reality is that there will be dwindling appetite and patience in the U.S. Congress -- and in the American body politic writ large -- to expend increasingly precious funds on behalf of nations that are apparently unwilling to devote the necessary resources or make the necessary changes to be serious and capable partners in their own defense," he said.
Without naming names, he blasted allies who are "willing and eager for American taxpayers to assume the growing security burden left by reductions in European defense budgets."
The U.S. has tens of thousands of troops based in Europe, not to stand guard against invasion but to train with European forces and promote what for decades has been lacking: the ability of the Europeans to go to war alongside the U.S. in a coherent way. The war in Afghanistan, which is being conducted under NATO auspices, is a prime example of U.S. frustration at European inability to provide the required resources.
"Despite more than 2 million troops in uniform, not counting the U.S. military, NATO has struggled, at times desperately, to sustain a deployment of 25,000 to 45,000 troops, not just in boots on the ground, but in crucial support assets such as helicopters, transport aircraft, maintenance, intelligence, surveillance and reconnaissance, and much more," Gates said.
Gates, a career CIA officer who rose to become the spy agency's director from 1991 to 1993, is retiring on June 30 after 4 1/2 years as Pentagon chief. His designated successor, Leon Panetta, is expected to take over July 1.
For many Americans, NATO is a vague concept tied to a bygone era, a time when the world feared a Soviet land invasion of Europe that could have escalated to nuclear war. But with the demise of the Soviet Union in 1991, NATO's reason for being came into question. It has remained intact -- and even expanded from 16 members at the conclusion of the Cold War to 28 today.
But reluctance of some European nations to expand defense budgets and take on direct combat has created what amounts to a two-tier alliance: the U.S. military at one level and the rest of NATO on a lower, almost irrelevant plane.
Gates said this could spell the demise of NATO.
"What I've sketched out is the real possibility for a dim, if not dismal future for the trans-Atlantic alliance," he said. "Such a future is possible, but not inevitable. The good news is that the members of NATO - individually and collectively - have it well within their means to halt and reverse these trends and instead produce a very different future."
Gates has said he believes NATO will endure despite its flaws and failings. But his remarks Friday point to a degree of American impatience with traditional and newer European allies that in coming years could lead to a reordering of U.S. defense priorities in favor of Asia and the Pacific, where the rise of China is becoming a predominant concern.
To illustrate his concerns about Europe's lack of appetite for defense, Gates noted the difficulty NATO has encountered in carrying out an air campaign in Libya.
"The mightiest military alliance in history is only 11 weeks into an operation against a poorly armed regime in a sparsely populated country, yet many allies are beginning to run short of munitions, requiring the U.S., once more, to make up the difference," he said.
His comment reflected U.S. frustration with the allies' limited defense budgets.
"To avoid the very real possibility of collective military irrelevance, member nations must examine new approaches to boosting combat capabilities," he said.
He applauded Norway and Denmark for providing a disproportionate share of the combat power in the Libya operation, given the size of their militaries. And he credited Belgium and Canada for making "major contributions" to the effort to degrade the military strength of Libya's Moammar Gadhafi.
"These countries have, with their constrained resources, found ways to do the training, buy the equipment and field the platforms necessary to make a credible military contribution," he said. But they are exceptions, in Gates' view.
A NATO air operations center designed to handle more than 300 flights a day is struggling to launch about 150 a day against Libya, Gates said.
On a political level, the problem of alliance purpose in Libya is even more troubling, he said.
"While every alliance member voted for the Libya mission, less than half have participated, and fewer than a third have been willing to participate in the strike mission," he said. "Frankly, many of those allies sitting on the sidelines do so not because they do not want to participate, but simply because they can't. The military capabilities simply aren't there."
Afghanistan is another example of NATO falling short despite a determined effort, Gates said.
He recalled the history of NATO's involvement in the Afghan war -- and the mistaken impression some allied governments held of what it would require of them.
"I suspect many allies assumed that the mission would be primarily peacekeeping, reconstruction and development assistance - more akin to the Balkans," he said, referring to NATO peacekeeping efforts there since the late 1990s. "Instead, NATO found itself in a tough fight against a determined and resurgent Taliban returning in force from its sanctuaries in Pakistan."
He also offered praise and sympathy, noting that more than 850 troops from non-U.S. NATO members have died in Afghanistan. For many allied nations these were their first military casualties since World War II.
He seemed to rehearse his position in the coming debate within the Obama administration on how many troops to withdraw from Afghanistan this year.
"Far too much has been accomplished, at far too great a cost, to let the momentum slip away just as the enemy is on his back foot," he said.
He said the "vast majority" of the 30,000 extra troops Obama sent to Afghanistan last year will remain through the summer fighting season. He was not more specific.
In a question-and-answer session with his audience after the speech, Gates, 67, said his generation's "emotional and historical attachment" to NATO is "aging out."
He said he is not sure what this means in practical terms. But if Europeans want to keep a security link to the U.S. in the future, he said, "the drift of the past 20 years can't continue."