The National Security Agency is winning its long-running secret war on encryption, using supercomputers, technical trickery, court orders and behind-the-scenes persuasion to undermine the major tools protecting the privacy of everyday communications in the Internet age, according to newly disclosed documents.

The agency has cracked much of the encryption, or digital scrambling, that guards global commerce and banking systems, protects sensitive data like trade secrets and medical records, and automatically secures emails, Web searches and phone calls of people around the world.

Many users assume — or have been assured by Internet companies — that their data is safe from prying eyes, including those of the government, and the NSA wants to keep it that way. The agency treats its recent successes in deciphering protected information as among its most closely guarded secrets, restricted to those cleared for a highly classified program code-named Bullrun, according to the documents, provided by Edward Snowden, the former NSA contractor.

Beginning in 2000, as encryption tools were gradually blanketing the Web, the NSA invested billions of dollars in a clandestine campaign to preserve its ability to eavesdrop. Having lost a public battle in the 1990s to insert its own “back door” in all encryption, it set out to accomplish the same goal by stealth.

The agency, according to the documents and interviews with industry officials, deployed custom-built, superfast computers to break codes, and began collaborating with technology companies in the United States and abroad to build entry points into their products. The documents do not identify which companies have participated.

The NSA hacked into target computers to snare messages before they were encrypted. In some cases, companies say they were coerced by the government into handing over their master encryption keys or building in a back door. And the agency used its influence as the world’s most experienced code maker to covertly introduce weaknesses into the encryption standards followed by hardware and software developers around the world.

“For the past decade, NSA has led an aggressive, multipronged effort to break widely used Internet encryption technologies,” said a 2010 memo describing a briefing about NSA accomplishments for employees of its British counterpart, Government Communications Headquarters, or GCHQ. “Cryptanalytic capabilities are now coming online. Vast amounts of encrypted Internet data which have up till now been discarded are now exploitable.”

When the British analysts, who often work side by side with NSA officers, were first told about the program, another memo said, “those not already briefed were gobsmacked!”

An intelligence budget document makes clear that the effort is still going strong.

“We are investing in groundbreaking cryptanalytic capabilities to defeat adversarial cryptography and exploit Internet traffic,” the director of national intelligence, James Clapper, wrote in his budget request for the current year.

In recent months, the documents disclosed by Snowden have described the NSA’s broad reach in scooping up vast amounts of communications around the world. The encryption documents now show, in striking detail, how the agency works to ensure that it is actually able to read the information it collects.

The agency’s success in defeating many of the privacy protections offered by encryption does not change the rules that prohibit the deliberate targeting of Americans’ emails or phone calls without a warrant. But it shows that the agency, which was sharply rebuked by a federal judge in 2011 for violating the rules and misleading the Foreign Intelligence Surveillance Court, cannot necessarily be restrained by privacy technology. NSA rules permit the agency to store any encrypted communication, domestic or foreign, for as long as the agency is trying to decrypt it or analyze its technical features.

NSA code-breaking

The NSA, which has specialized in code-breaking since its creation in 1952, sees that task as essential to its mission. If it cannot decipher the messages of terrorists, foreign spies and other adversaries, the United States will be at serious risk, agency officials say.

Just in recent weeks, the Obama administration has called on the intelligence agencies for details of communications by al-Qaida leaders about a terrorist plot and of Syrian officials’ messages about the chemical weapons attack outside Damascus, Syria. If such communications can be hidden by unbreakable encryption, NSA officials say, the agency cannot do its work.

But some experts say the NSA’s campaign to bypass and weaken communications security may have serious unintended consequences. They say the agency is working at cross-purposes with its other major mission, apart from eavesdropping: ensuring the security of U.S. communications.

Some of the agency’s most intensive efforts have focused on the encryption in universal use in the United States, including Secure Sockets Layer, or SSL, virtual private networks, or VPNs, and the protection used on fourth generation, or 4G, smartphones. Many Americans, often without realizing it, rely on such protection every time they send an email, buy something online, consult with colleagues via their company’s computer network, or use a phone or a tablet on a 4G network.

For at least three years, one document says, GCHQ, almost certainly in close collaboration with the NSA, has been looking for ways into protected traffic of the most popular Internet companies: Google, Yahoo, Facebook and Microsoft’s Hotmail. By 2012, GCHQ had developed “new access opportunities” into Google’s systems, according to the document. (Google denied giving any government access and said it had no evidence that its systems had been breached.)

Paul Kocher, a leading cryptographer who helped design the SSL protocol, recalled how the NSA lost the heated national debate in the 1990s about inserting into all encryption a government back door called the Clipper Chip.

“And they went and did it anyway, without telling anyone,” Kocher said.

A vital capability

The documents are among more than 50,000 shared by The Guardian with The New York Times and ProPublica, the nonprofit news organization. They focus primarily on GCHQ but include thousands either from or about the NSA.

Intelligence officials asked the Times and ProPublica not to publish this article, saying it might prompt foreign targets to switch to new forms of encryption or communications that would be harder to collect or read. The news organizations removed some specific facts but decided to publish the article because of the value of a public debate about government actions that weaken the most powerful tools for protecting the privacy of Americans and others.

The files show that the agency is still stymied by some encryption, as Snowden suggested in a question-and-answer session on The Guardian’s website in June.

“Properly implemented strong crypto systems are one of the few things that you can rely on,” he said, though cautioning that the NSA often bypasses the encryption altogether by targeting the computers at one end or the other and grabbing text before it is encrypted or after it is decrypted.

The documents make clear that the NSA considers its ability to decrypt information a vital capability, one in which it competes with China, Russia and other intelligence powers.

“In the future, superpowers will be made or broken based on the strength of their cryptanalytic programs,” a 2007 document said. “It is the price of admission for the U.S. to maintain unrestricted access to and use of cyberspace.”

The full extent of the NSA’s decoding capabilities is known only to a limited group of top analysts from the so-called Five Eyes: the NSA and its counterparts in Britain, Canada, Australia and New Zealand. Only they are cleared for the Bullrun program, the successor to one called Manassas — both names of a U.S. Civil War battle. A parallel GCHQ counterencryption program is called Edgehill, named for the first battle of the English Civil War of the 17th century.

Ties to Internet companies

When the NSA was founded, encryption was an obscure technology used mainly by diplomats and military officers. During the past 20 years, with the rise of the Internet, it has become ubiquitous. Even novices can tell that their exchanges are being automatically encrypted when a tiny padlock appears next to the Web address on their computer screen.

Because strong encryption can be so effective, classified NSA documents make clear, the agency’s success depends on working with Internet companies — by getting their voluntary collaboration, forcing their cooperation with court orders or surreptitiously stealing their encryption keys or altering their software or hardware.

Since Snowden’s disclosures ignited criticism of overreach and privacy infringements by the NSA, U.S. technology companies have faced scrutiny from customers and the public over what some see as too cozy a relationship with the government. In response, some companies have begun to push back against what they describe as government bullying.

Google, Yahoo, Microsoft and Facebook have pressed for permission to reveal more about the government’s secret requests for cooperation. One small email encryption company, Lavabit, shut down rather than comply with the agency’s demands for what it considered confidential customer information; another, Silent Circle, ended its email service rather than face similar demands.

Ladar Levison, the founder of Lavabit, wrote a public letter to his disappointed customers, offering an ominous warning.

“Without congressional action or a strong judicial precedent,” he wrote, “I would strongly recommend against anyone trusting their private data to a company with physical ties to the United States.”