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WASHINGTON — Last month, some of President Barack Obama’s top intelligence advisers met in Silicon Valley with Apple’s Timothy D. Cook and other technology leaders in what seemed to be a public rapprochement in their long-running dispute over the encryption safeguards built into their devices.

But behind the scenes, relations were tense, as lawyers for the Obama administration and Apple held closely guarded discussions for over two months about one particularly urgent case: The FBI wanted Apple to help “unlock” an iPhone used by one of the two attackers who killed 14 people in San Bernardino, California, in December, but Apple was resisting.

When the talks collapsed, a federal magistrate judge, at the Justice Department’s request, ordered Apple to bypass security functions on the phone, setting off a furious public battle Wednesday between the Obama administration and one of the world’s most valuable companies in a dispute with far-reaching legal and implications.

“This Apple case really goes right to the heart of the encryption issue,” said Ira Rubinstein, a senior fellow at New York University’s Information Law Institute, “and in some ways, this was a fight that was inevitable.”

This is not the first time a technology company has been ordered to effectively de-encrypt its own product, but industry experts say it is surely the most significant because of Apple’s huge global profile, the invasive steps it says are being demanded, and the notoriety of the San Bernardino attacks.

Law enforcement officials who support the FBI’s position said that the impasse with Apple provides an ideal test case to move the long-simmering encryption issue from an abstract debate over the balance between national security and privacy to a concrete one.

With the FBI’s inability to get into the phone used by Syed Rizwan Farook, who was killed by the police along with his wife after they attacked Farook’s co-workers at a holiday gathering, “the worst case scenario has come true,” said Reynaldo Tariche, an FBI agent on Long Island who is president of the agents’ association. “As more of these devices come to market, this touches all aspects of the cases that we’re working on.”

Magistrate Judge Sheri Pym of the U.S. District Court for the District of Central California issued her order after the FBI said it had been unable to access the data in the phone on its own and needed Apple’s technical assistance to work around the encryption software protecting it.

Cook, the chief executive at Apple, responded with a blistering, 1,100-word letter to Apple customers, warning of the “chilling” breach of privacy posed by the government’s demands. He maintained that the order would effectively require it to create a “backdoor” to get around its own safeguards, and Apple vowed to appeal the ruling by next week.

“The same engineers who built strong encryption into the iPhone to protect our users would, ironically, be ordered to weaken those protections and make our users less safe,” Cook said.

Apple argues that the software the FBI wants it to create does not exist. But technologists say the company can do it.

Cook’s angry tone reflected the tense discussions, conducted mostly on the telephone, between his company and the government’s lawyers over the San Bernadino case.

Apple executives had hoped to resolve the impasse without having to rewrite their own encryption software, and they were frustrated by the Justice Department’s refusal to file its demands under seal rather than airing them publicly in court, according to an industry executive with knowledge of the case, who spoke on condition of anonymity in discussing internal discussions.

The Justice Department and the FBI have the White House’s “full support,” the spokesman, Josh Earnest, said Wednesday.

His vote of confidence was significant because James Comey, the FBI director, has at times been at odds with the White House over his aggressive advocacy of tougher decryption requirements on technology companies. While Obama’s national security team was sympathetic to Comey’s position, others at the White House viewed legislation as potentially fraught. Late last year, Obama refused to back any legislation requiring decryption, leaving a court fight like the one playing out now with Apple as a likely situation.

The dispute could initiate legislation in Congress, with Republicans and Democrats alike criticizing Apple’s stance on Wednesday and calling for tougher decryption requirements. Donald Trump, the Republican presidential contender, also attacked Apple on Fox News, asking: “Who do they think they are?”

But Apple had many defenders of its own among privacy and consumer advocates, who praised Cook for standing up to what they saw as government overreach.

Many of the company’s defenders argued that the types of government surveillance operations exposed in 2013 by Edward Snowden, the former National Security Agency contractor, have prompted technology companies to build tougher encryption safeguards in their products because of the privacy demands of their customers.

“Apple deserves praise for standing up for its right to offer secure devices to all of its customers,” said Alex Abdo, staff lawyer for the American Civil Liberties Union’s privacy and technology section.

Privacy advocates and others said they worried that if the FBI succeeded in getting access to the software overriding Apple’s encryption, it would create easy access for the government in many future investigations.

“This is not the last step in the journey,” said Robert Cattanach, a former Justice Department lawyer who works on privacy and cybersecurity issues at the law firm of Dorsey & Whitney. “The next thing you know, they’ll be in the back door of these systems.”

The Apple order is a flashpoint in a dispute that has been building for more than a decade.

The FBI began sounding alarms years ago about technology that allowed people to exchange private messages protected by encryption so strong that government agents could not break it. In the fall 2010, at the behest of Robert S. Mueller III, the FBI director at the time, the Obama administration began work on a law that required technology companies to provide unencrypted data to the government.

Lawyers at the FBI and the Justice and Commerce departments drafted bills around the idea that technology companies in the Internet age should be bound by the same rules as phone companies, which were forced during the Clinton administration to build digital networks that government agents could tap.

The draft legislation would have covered app developers such as WhatsApp and large companies such as Google and Apple, according to current and former officials involved in the process.

Administration officials involved in drafting the legislation argued that, when armed with a court order, the government should able to get access to text messages and other data stored in plain text. Far less certain was whether the government could use a court order to force a company to write software or redesign its system was far less clear. A federal law would make that authority clear, they said.

But the disclosures of government surveillance by Snowden, the former National Security Agency employee and contractor, dramatically changed the privacy debate and the Obama administration decided not to go ahead with the proposed legislation. It has yet to be revived.

The legal issues raised by the judge’s order are complicated. They involve statutory interpretation, rather than constitutional rights, and they could end up before the Supreme Court.

As Apple noted, the FBI, instead of asking Congress to pass legislation resolving the encryption fight, has proposed what appears to be a novel reading of the All Writs Act of 1789.

The law lets judges “issue all writs necessary or appropriate in aid of their respective jurisdictions and agreeable to the usages and principles of law.”

The government says the law gives broad latitude to judges to require “third parties” to execute court orders. It has cited, among other cases, a 1977 ruling requiring phone companies to help set up a pen register, a device that records all numbers called from a particular phone line.

Apple, in turn, argues that the scope of the act has strict limits. In 2005, a federal magistrate judge rejected the argument that the law could be used to compel a telecommunications provider to allow real-time tracking of a cellphone without a search warrant.