The Financial Times reports Gates is going against the grain of other technology giants like Facebook and Twitter who backed Apple's stance to not give the government a "backdoor" into its products.
"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 told the Financial Times.
"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, who has distanced himself from Microsoft for world philanthropy, is going against Microsoft's own backing of Apple last week.
Federal agents have been trying to gain access to the iPhone since Farook and his wife, Tashfeen Malik, killed 14 people and injured dozens in the shooting attack on December 2.
The FBI said it's unable to unlock the iPhone in question because it's locked with a passcode. Last week, a judge ruled Apple must provide "reasonable technical assistance" to help agents unlock the phone.
Tim Cook, CEO of Apple, has been vocal in opposing the ruling.
"We feel the best way forward would be for the government to withdraw its demands under the All Writs Act and, as some in Congress have proposed, form a commission or other panel of experts on intelligence, technology and civil liberties to discuss the implications for law enforcement, national security, privacy and personal freedoms," Cook told employees in a letter obtained by BuzzFeed.
Update: In a statement to Bloomberg on Tuesday, Gates says he was blindsided by the headlines he backed the FBI:
I do believe that with the right safeguards, there are cases where the government, on our behalf, like stopping terrorism, which could get worse in the future, that that is valuable. But striking that balance--clearly the government has taken information historically and used it in ways we didn't expect, going all the way back to say the FBI under J. Edgar Hoover. I'm hoping now we can have the discussion. I do believe there are sets of safeguards where the government shouldn't have to be completely blind. The courts are going to decide this. And I think Apple said that whatever the final court decision is, they'll abide by. In the meantime, that gives us this opportunity to get the discussion and these issues will be decided in Congress. The Patriot Act, how that gets evolved. You don't want to just take the minute after a terrorist event and swing that direction, nor do you want to in general completely swing away from government access when you get some abuse being revealed. You want to strike that balance that the United States leads in setting example."