Referee Darren Drysdale has been charged with improper conduct over his confrontation with Ipswich midfielder Alan Judge.
The 49-year-old Lincolnshire official appeared to square up to Judge and lean his head into the Republic of Ireland international after the midfielder's appeal for a penalty had been turned down during Ipswich's goalless draw with Northampton on Tuesday evening.
Drysdale apologised to both Judge and Ipswich for his actions on Wednesday afternoon but the FA has now charged him with improper conduct.
"It is alleged that the match official's behaviour during the 90th minute of the game amounts to improper conduct and he has until Thursday 4 March 2021 to provide a response."
Drysdale had said in his earlier statement, released by the Professional Game Match Officials Limited before he was charged by the FA: "I fully understand that it is important for us as referees to maintain our composure throughout the game and always engage with players in a professional manner.
"I'm sorry that I did not do that last night and I can only apologise to Alan and Ipswich Town."
The PGMOL statement added: "As The FA are now investigating the incident in line with their usual disciplinary process it would not be appropriate to make any further comments."
Ipswich manager Paul Lambert had earlier on Wednesday called for the matter to be investigated.
Lambert told talkSPORT: "I've text Mike Jones (EFL head of referees) this morning to say have a look at the footage of the head thing.
"To me, in my opinion, it looks as if the referee went in there and I said to him after the game, 'Did you put your head in my player?'
"He couldn't answer it and that's the reason I spoke to Mike. I haven't seen that in a long, long while."
The incident occurred towards the end of Ipswich's goalless draw with Northampton at Portman Road.
Ipswich pair Flynn Downes and Jack Lankester and Northampton defender Lloyd Jones stepped in and calmed the situation before Drysdale booked Judge.
Drysdale, who was appointed to the National List of referees covering EFL games in 2004, has also been a FIFA and UEFA assistant referee and was an assistant referee at the 2000 FA Cup final.
The referee has received support from a number of players on social media, including Aston Villa's England internationals Jack Grealish and Tyrone Mings.
Grealish wrote: "Ah come on?! No need to apologise at all! I think it's brilliant."
And his team-mate Mings believes more needs to be done to ensure referees receive respect from players.
"Refs and officials put up with a lot from players. I'm sure he isn't proud of it but in the world we're living in, I think you can allow for some compassion when people don't always act as they should," Mings replied to a tweet.
"I agree that they should be impartial. But methodical? They are human and like I said, some of the stuff said to them isn't nice. It probably highlights how professional they are and how well of a job they do that more of them haven't reacted like that."
In response to a tweet drawing comparisons with rugby, he added: "Completely agree. Would love to hear refs mic'd up for more transparency on decisions. Think it would clear up a lot of confusion and hopefully reduce frustration. Works brilliantly in rugby."