The singer posted a stream of messages on Twitter about the incident along with a picture, before deleting them.
"N****s throwing bottles! Y'all n****z weak!," he said.
"OK N****s stand behind security!!!! Ok! U don't pay them enough."
He continued: "N****s hiding in the bathroom bitch ass n****s! And I'm the singer?
"Bottles? It's nothing! Lol. N****s is p***y... How u party wit a rich n***a that hate? Lol.... Throwing bottles like girls? #shameonya!"
The image and the comment "Bottles? It's nothing! Lol" are still visible on Brown's f**kyopictures Instagram page.
Several witnesses have said that the bottle came from an area of the club where Brown's supposed rival Drake was present, Rap-Up reports.
According to MediaTakeOut, the incident occurred when Brown sent a bottle of champagne to Drake's table.
It is alleged, but unconfirmed, that the bottle was then returned with a note reading: "I'm f**king the love of your life, deal with it."
It is claimed that the note is referring to Rihanna, Brown's former partner who has recorded several tracks with Drake.
Brown and Rihanna split in 2008 after he pleaded guilty to a felony assault on Rihanna, though the pair were later rumoured to have rekindled their relationship and appeared on remixes of each other's songs earlier this year.