Arsenal lost for the first time in the Premier League this season a fortnight ago following a contentious goal by Anthony Gordon.
Arteta labelled the decision to allow the goal to stand as a disgrace and embarrassing.
The goal was deemed legitimate despite a lengthy VAR check to decide whether the ball had gone out of play in the build up to the goal, a foul on Arsenal defender Gabriel Magalhaes on Joelinton and a possible offside by Gordon.
A statement from the FA on Thursday read: "Mikel Arteta has been charged with a breach of FA rule E3.1 following comments that he made in media interviews after Arsenal's Premier League game against Newcastle United on Saturday 4 November.
"It's alleged that his comments constitute misconduct as they are insulting towards match officials and/or detrimental to the game and/or bring the game into disrepute.
"Mikel Arteta has until Tuesday 21 November to provide a response to the charge."
Arsenal have since released a statement to back their manager's comments.
