Earlier this week, the 'Kiss Kiss' hitmaker was reportedly detained by Parisian police after a 24-year-old woman claimed she was sexually assaulted at the singer's hotel suite.
Brown denied the allegations in a now-deleted Instagram post which read: "this b!tch is lyin'."
Following his release from custody on Tuesday (local time), he uploaded a video of a dance rehearsal captioned: "We Working," prompting Bieber to chime in with a message of encouragement.
"No one can touch you, ur [sic] the GOAT [Greatest Of All Time]," he commented.
Comedian Nick Cannon also backed Brown, writing: "Stay Focused King!"
According to Cosmopolitan, some of Bieber's fans were upset with his public affirmation of Brown, who has a history of alleged violent crime including pleading guilty to savagely assaulting his then-girlfriend Rihanna in 2009.
"Justin you missed the incredible opportunity to stay silent," one Instagram user wrote.
"The fact that you're supporting a rapist, a known abuser, makes me sick to my stomach. I looked up to you, and this is honestly so disappointing... please educate yourself on the topic."
"Omg Justin Bieber has been cancelled," said another.
TMZ reports that Brown's latest accuser described the assault as "brutal and violent", claiming she was also abused by the singer's bodyguard and friends afterwards.
The gossip website added that Brown intends to sue the woman for defamation.