The war of words between Apple and the government continued Monday as FBI Director James Comey said forcing Apple to help unlock the iPhone of one of the San Bernardino shooters is no big deal.

"We don't want to break anyone's encryption or set a master key loose on the land," Comey said in a statement Sunday night, insisting that vital decisions involving safety from terrorists shouldn't be left in the hands of "corporations that sell stuff for a living."

Read MoreFBI fires back at Apple: 'We don't want to break anyone's encryption

In a letter to his employees Monday, Apple ceo Tim Cook said "this case is about much more than a single phone or a single investigation…At stake is the data security of hundreds of millions of law-abiding people."

Eli Dourado, director of technology policy at George Mason University's Mercatus Center, told CNBC on Monday that the long-simmering battle between law enforcement and Silicon Valley is about to get even more complex.

"If the FBI gets a new weapon in its legal tool-kit, it could set a chilling precedent for companies all around the world," said Dourado. "While it might be easy for a company the size of Apple to square off against the FBI, smaller companies will have a harder time saying "no" to them. And that would be a troubling turn of events."

Read MoreWhy Apple is right to fight FBI backdoor

Claude Barfield, resident scholar with American Enterprise Institute, said a potential government victory over Apple will also have wide-reaching repercussions in the White House.

"The Justice Department's action should impel the Obama Administration to make a definitive statement on encryption, The President publicly considered the need for legislation and then backed off," said Barfield. "Whatever the legal complexities, good policy dictates clear justification for the Administration's legal action. The President should take that advice."