The message is accompanied by an online question-and-answer page that reiterates many of the comments Mr Cook made in a public letter after a magistrate judge’s order last week.
It also dismisses several key government claims, including an assertion that the company was acting out of business interests in saying it would not co-operate with an FBI investigation of the shootings.
A magistrate has ordered the company to break its iPhone security protocols to aid federal officials probing the December shootings.
The legal fight has sparked a debate on government power, digital rights, public safety, and security.
The iPhone was used by Syed Farook, who along with wife Tashfeen Malik, killed 14 people in the attack.
Mr Cook states in the letter to employees that the company has “no tolerance or sympathy for terrorists” and believes abiding by the judge’s order would be unlawful and an expansion of government powers, and would set a dangerous precedent that would essentially create a backdoor to the encrypted iPhone.
“This case is about much more than a single phone or a single investigation,” said Mr Cook.
“At stake is the data security of hundreds of millions of law-abiding people and setting a dangerous precedent that threatens everyone’s civil liberties.”
The email acknowledges that it is technically possible for Apple to do what the judge ordered, but that it is “something we believe is too dangerous to do”.
Apple also raised the difficulty of keeping a “master key” safe once created.
The US has said Apple could keep the specialised technology it would create to help officials hack the phone, bypassing a security time delay and feature that erases all data after 10 consecutive unsuccessful attempts to guess the passcode.
If Apple’s engineers were to do as ordered, Apple would do its best to protect the technology, but Mr Cook said that the company “would be relentlessly attacked by hackers and cybercriminals”.