The US Government now has to weigh whether to disclose the flaws to Apple, a decision that probably will be made by a White House-led group.
The people who helped the US Government come from the sometimes shadowy world of hackers and security researchers who profit from finding flaws in companies' software or systems.
Some hackers, known as "white hats," disclose the vulnerabilities to the firms responsible for the software or to the public so they can be fixed and are generally regarded as ethical. Others, called "black hats," use the information to hack networks and steal people's personal information.
The individuals who helped the FBI in the San Bernardino, California, case fall into a third category, often considered ethically murky: researchers who sell flaws to governments, companies that make surveillance tools or groups on the black market.
This last group, dubbed "grey hats," can be controversial since critics say they might be helping governments spy on their own citizens. When selling exploits to governments or on the black market, researchers do not disclose the flaws to the companies responsible for the software, as the exploits' value depends on the software remaining vulnerable.
In the case of the San Bernardino iPhone, the solution found by the hackers has limited shelf life.
FBI Director James Comey has said that the solution works only on iPhone 5Cs running the iOS 9 operating system - what he calls a "narrow slice" of phones.
Apple said last week that it would not sue the Government to gain access to the San Bernardino solution.
Still, many security and privacy experts have been calling on the Government to disclose the vulnerability data to Apple so that the firm can patch it.
If the Government shares data on the flaws with Apple, "they're going to fix it and then we're back where we started from," Comey said in a discussion at a privacy conference last week. Nonetheless, he said on Tuesday, "we're considering whether to make that disclosure or not."
The White House has established a process in which federal officials weigh whether to disclose any security vulnerabilities they find. It could be weeks before the FBI's case is reviewed, officials said.
We do have an intelligence and national security mission that we have to carry out
"When we discover these vulnerabilities, there's a very strong bias towards disclosure," White House cybersecurity coordinator Michael Daniel said in an interview in October 2014, speaking generally and not about the Apple case. "That's for a good reason. If you had to pick the economy and the government that is most dependent on a digital infrastructure, that would be the United States."
But, he added, "we do have an intelligence and national security mission that we have to carry out. That is a factor that we weigh in making our decisions."
The decision-makers, which include senior officials from the Justice Department, FBI, National Security Agency, CIA, State Department and Department of Homeland Security, consider how widely used the software in question is. They also look at the utility of the flaw that has been discovered. Can it be used to track members of a terrorist group, to prevent a cyberattack, to identify a nuclear weapons proliferator? Is there another way to obtain the information?
In the case of the phone used by the San Bernardino terrorist, "you could make the justification on both national security and on law enforcement grounds because of the potential use by terrorists and other national security concerns," said a senior administration official.
A decision also can be made to disclose the flaw - just not right away. An agency might say it needs the vulnerability for only a few months or that its utility will quickly diminish.
"A decision to withhold a vulnerability is not a forever decision," Daniel said in the earlier interview. "We require periodic reviews. So if the conditions change, if what was originally a true [undiscovered flaw] suddenly becomes identified, we can make the decision to disclose it at that point."