Arsenal head coach Unai Emery has been charged with improper conduct by the FA over the bottle kicking incident at Brighton on Boxing Day.
Sky Sports News reported earlier on Thursday that the Football Association were investigating the incident for which Emery subsequently apologised.
Emery kicked the bottle in frustration during the 1-1 draw with Chris Hughton's side at the Amex Stadium.
An FA statement read: "Arsenal manager Unai Emery has been charged following the game against Brighton yesterday [26 December 2018]. It is alleged his action of kicking a water bottle during the fixture amounts to improper conduct."
Emery later admitted that the bottle hit a supporter, however, the incident is not thought to have been included in the referee's match report.
"I say yesterday [Wednesday] my apologies, I kicked the bottle in frustration but not for the supporter, I kicked for me and it went near to the supporter and I said to them my apologies," he said. "There is not another communication.
"I repeat today my apologies for my individual action but I kick the bottle because it is near me, but not because it is my intention."
Emery then said he would respect any decision the FA made, although he was keen to draw a line under the incident.
"I hope so, yes," he replied when asked whether his apology would mean he would not face official censure.
"But I have to respect the decision because it is a circumstance of my action but not another intention from me with the supporter. I say to them my apology."
He has until 6pm on January 2 to respond.