Apple ( AAPL ) CEO Tim Cook has taken a hard line against government efforts to unlock password-protected smartphones. But Apple’s pushback to a new federal demand this week could stymie the San Bernardino, Calif., terrorist investigation. This twist puts the company at the center of a long clash with government over technology industry security and privacy, and in a public relations pickle. In an open letter to customers late Tuesday, Cook vowed to resist government orders to break its smartphone encryption. He said there is much more at stake than complying with one government request to access data on one iPhone. A federal judge on Tuesday ordered Apple to provide “reasonable technical assistance” to the FBI to unlock an iPhone belonging to one of the killers in the San Bernardino shootings. The order calls for Apple to create software that can get around or disable the security option that erases data from an iPhone after 10 unsuccessful attempts to unlock it. Syed Farook and his wife, Tashfeen Malik, shot and killed 14 people on Dec. 2. The radicalized Muslim couple, described in press reports as supporters of terror group ISIS, later died in a gun battle with police. Complying with the court’s order would create a “dangerous precedent,” Cook said. The government’s demands threaten the security of all of its customers, he said. “Some would argue that building a backdoor for just one iPhone is a simple, clean-cut solution. But it ignores both the basics of digital security and the significance of what the government is demanding in this case,” Cook said. “While the government may argue that its use would be limited to this case, there is no way to guarantee such control.” If the backdoor becomes available, hackers and criminals will try to exploit it, Cook said. And the federal government, which has shown a willingness to spy on its own citizens through the National Security Agency, also could seek more access to smartphones. Cook said he believes the FBI’s intentions here are good, but that ramifications of their demands are too far-reaching to ignore. “The implications of the government’s demands are chilling,” Cook said. “The government could extend this breach of privacy and demand that Apple build surveillance software to intercept your messages, access your health records or financial data, track your location, or even access your phone’s microphone or camera without your knowledge.” Cook said Apple has no sympathy for terrorists and has cooperated with the FBI to the best of its ability. The court says it isn’t asking Apple to break the phone’s encryption, but rather to “bypass or disable the auto-erase function whether or not it has been enabled.” That way, the government can try to crack the password using “brute force” — electronically entering millions of combinations without risking deletion of the data. The Electronic Frontier Foundation, a leading nonprofit organization that defends civil liberties in the digital world, has come out in support of Apple in the case. “For the first time, the government is requesting Apple write brand new code that eliminates key features of iPhone security – security features that protect us all,” Kurt Opsahl, deputy executive director and general counsel for the EFF, said in a blog post . “Essentially, the government is asking Apple to create a master key so that it can open a single phone. And once that master key is created, we’re certain that our government will ask for it again and again, for other phones, and turn this power against any software or device that has the audacity to offer strong security.” Opsahl went on to note that “once this master key is created, governments around the world will surely demand that Apple undermine the security of their citizens as well.” Digital rights group Fight for the Future also has spoken out about the federal court order. “Governments have been frothing at the mouth hoping for an opportunity to pressure companies like Apple into building backdoors into their products to enable more sweeping surveillance. It’s shameful that they’re exploiting the tragedy in San Bernardino to push that agenda,” Evan Greer, Fight for the Future’s campaign director, said in a blog post . “Security experts agree that any weakening or circumvention of security features on a phone puts everyone in danger.” Wendy Patrick, a business ethics and legal expert on the faculty at San Diego State University, said the Apple case raises the question of whether we can have digital security when there are national security concerns. “The public may have to give up some measure of digital privacy to make sure we stay safe from terrorists,” Patrick told IBD. “A lot of people believe that national security is paramount.” But Apple is worried about damaging its relationship with its customers if it makes iPhones vulnerable to hackers and government snoops. It sees the creation of a slippery slope by setting a precedent in this case, she said. U.S. Magistrate Judge Sheri Pym gave Apple five days to contest her ruling on the grounds that it might be unduly burdensome. Apple is likely to do so and the case could be at a stalemate for some time, Patrick said. Image provided by Shutterstock .