Zeid Ra'ad Al Hussein's intervention came after Apple's largest rivals backed the tech giant's bid to resist the US government demand seeking to access the iPhone used by one of the attackers in a deadly rampage in San Bernardino, California in December.
"In order to address a security-related issue related to encryption in one case, the authorities risk unlocking a Pandora's Box that could have extremely damaging implications for the human rights of many millions of people, including their physical and financial security," Zeid said in a statement.
The FBI wants to unlocked the iPhone used by Syed Farook, who was behind the San Bernardino massacre along with his wife Tashfeen Malik that left 14 people dead.
The agency has argued that by introducing encryption that can lock data, making it accessible only to the user, Apple and other tech companies are essentially creating "warrant-proof zones" for criminals and others that will cripple law enforcement and jeopardise public security.
Zeid said the FBI "deserves everyone's full support" in its investigation into what he described as an "abominable crime".
But he added: "This case is not about a company -- and its supporters -- seeking to protect criminals and terrorists, it is about where a key red line necessary to safeguard all of us from criminals and repression should be set.
"There are many ways to investigate whether or not these killers had accomplices besides forcing Apple to create software to undermine the security features of their own phones.
Zeid said encryption tools were widely used around the world, including by human rights defenders, civil society, journalists, whistle-blowers and political dissidents facing persecution and harassment.
"Encryption and anonymity are needed as enablers of both freedom of expression and opinion, and the right to privacy. Without encryption tools, lives may be endangered."
Three tech associations representing Apple's main business rivals - including Google, Facebook, Microsoft and Yahoo- said they supported Apple's efforts to challenge the order.
