"This is a specific case where the government is asking for access to information. They are not asking for some general thing, they are asking for a particular case," Gates said.

"It is no different than [the question of] should anybody ever have been able to tell the phone company to get information, should anybody be able to get at bank records. Let's say the bank had tied a ribbon round the disk drive and said 'don't make me cut this ribbon because you'll make me cut it many times'."

Gates' stance sets him apart from other tech executives on the issue. Facebook founder Mark Zuckerberg, Twitter founder Jack Dorsey and the head of Google, Sundar Pichari, have sided with Cook.

Former NSA and CIA director Michael Hayden told CNBC on Tuesday the government would be giving intelligence services one more entryway into Americans' data should it prevail in the dispute.

"America is more secure — America is more safe — with unbreakable end-to-end encryption," Hayden told CNBC's "Squawk Box."