Referee Darren Drysdale has apologised for his confrontation with Ipswich midfielder Alan Judge on Tuesday.
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 the League One match.
"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," Drysdale said in a statement released by the Professional Game Match Officials Limited.
"I'm sorry that I did not do that last night and I can only apologise to Alan and Ipswich Town."
The incident occurred towards the end of Ipswich's goalless draw with Northampton at Portman Road.
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."
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.