After the Federal Bureau of Investigation was able to crack Farook's iPhone, other authorities used third-party services like Grayshift - which was founded by a former Apple engineer - and Cellebrite to open locked iPhones.
The move by Apple, the latest in an ongoing clash with law enforcement, comes amid reports of growing use of a tool known as GrayKey which can enable police to bypass iPhone security features.
Security researchers estimate that the changes to the iPhone's operating system code could cut access to devices by as much as 90%.
Apple has butted heads with law enforcement about unlocking iPhones before.
"We're constantly strengthening the security protections in every Apple product to help customers defend against hackers, identity thieves and intrusions into their personal data", Apple spokesman, Fred Sainz, said in an email quoted by the New York Times.
On Wednesday, Apple said it was aware of the vulnerability and made a decision to patch it.
An Apple Store staff shows Apple's new iPhones X after they go on sale at the Apple Store in Regents Street, London, Britain, November 3, 2017.
"Apple is redesigning chargers and related interface for its next-generation iPhone and iPad devices, and will likely have its 2019 series of iPhones come with USB Type-C support". Law enforcement officials said they generally send iPhones to Cellebrite to unlock, with each phone costing several thousand dollars to open.
With the changes, police or hackers will typically have an hour or less to get a phone to a cracking machine.
A legal standoff followed the 2015 San Bernardino shooting, sparking a debate about whether Apple should install backdoors for forensics teams to access data on iPhone quickly -in this case, specifically on the iPhone of the shooter, who killed 14 people in the attack.
The FBI didn't immediately respond to a request for comment.