Referee Darren Drysdale apologises for locking heads with Ipswich Town midfielder Alan Judge.
In a statement by the Professional Game Match Officials Limited (PGMOL), 49-year-old Drysdale said he “did not maintain his composure”.
The Lincolnshire official moved his head towards Judge late in the game and briefly appeared to square up to him.
“I can only apologise to Alan and Ipswich Town,” Drysdale said.
“I fully understand 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.”
PGMOL confirmed the incident during Tuesday’s League One fixture is now also being investigated by the Football Association.
“In line with their usual disciplinary process, it would not be appropriate to make any further comments,” a PGMOL spokesperson said.
Northampton’s Lloyd Jones led Drysdale away from the confrontation, which happened in added time at Portman Road.
Republic of Ireland midfielder Judge, 32, was booked for simulation shortly after and a couple of minutes later his team-mate Flynn Downes was sent off for violent conduct.
Drysdale showed five yellow cards and a red card during the game. Ipswich manager Paul Lambert has also asked the EFL to investigate the confrontation.