The Justice Department is presently tying to force Apple into creating a one-off software program that will allow FBI investigator to crack the iPhone password of San Bernardino suspect Syed Farook.
Also, that's what has Apple and other tech companies anxious - a legal precedent greatly expanding the limits of what the government can force a company to do.
In the NY case, Magistrate Judge James Orenstein on Monday denied a request by the Department of Justice to compel Apple to bypass the passcode security on an iPhone tied to a convicted drug trafficker.
The California case involves an iPhone 5C owned by San Bernardino County and used by Syed Farook, who was a health inspector.
Federal agents in NY wanted a court order requiring Apple to help them get around the password security feature on an iPhone 5 that belonged to a confessed drug dealer.
But while this may be a different case, the ruling may set a precedent strengthening the Apple's argument that it doesn't have to cooperate with a February 16 court order to hack into the terrorist's iPhone. In that case, the phone used an older version of iOS that Apple could unlock without new software.
In the California case, Apple isn't the only one trying to sway the judge.
"I think we can come up with a solution where we can accomplish all of our goals in protecting our country and protecting people's data and allowing our companies to be competitive", said Staten Island Congressman Dan Donovan.
U.S. Magistrate Judge James Orenstein's written decision gives support to the company's position in its fight against a California judge's order that it create specialized software to help the FBI hack into an iPhone linked to the San Bernardino terrorism investigation.
The investigating agency still believes that encrypted data in Farook's phone and its GPS system is likely to have significant clues about what happened after the shootings.
Comey went on to say that the Federal Bureau of Investigation was highly concerned about "warrant-proof spaces", and that tech companies such as Apple shouldn't be permitted to create such spaces through impenetrable encryption. Still, Mr Comey said, "The experts tell me there's no way we would have gotten everything off the phone from a backup".
Sewell said Apple didn't have a proposed solution, but was willing to participate in efforts to find one.
Apple's lawyer Bruce Sewell warned that the government is forcing Apple to weaken the security of its products with potentially catastrophic consequences.
Apple's opposition to the government's tactics has evoked a national debate over digital privacy rights and national security.
Manhattan District Attorney Cyrus Vance, who will also be testifying Tuesday, previously said his office has 175 phones it is unable to unlock - and told Charlie Rose he would "absolutely" push forward for access to them if the government prevailed in the case.