Ipswich have demanded that an investigation is made into referee Darren Drysdale after footage appeared to show the official leaning his head towards Blues player Alan Judge.
The 49-year-old appeared to square up to Ipswich's Judge after an appeal for an penalty was rejected during the Blues' League One tie with Northampton on Tuesday.
Ipswich boss Paul Lambert confirmed that the club have contacted the EFL over the alleged incident and the Blues have demanded an investigation into the matter.
Lambert told talkSPORT on Wednesday: 'I've texted 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 EFL have confirmed to Sportsmail that they are aware of the incident and that the PGMOL are in discussion with all parties. The FA have told Sportsmail they too are aware of the incident.
The official booked Judge for simulation after the scuffle involving Drysdale, while the referee also sent off Blues player Flynn Downes for a second bookable offence in stoppage time.
Drysdale is in line to take charge of Southend United's match with Bolton Wanderers this weekend though the official's involvement in the game is now in doubt after these allegations.
Former Premier League referee Mark Halsey told The Sun that Drysdale 'should NEVER put himself in that position' at Portman Road.
Halsey said: 'I'm sure the PGMOL will conduct an investigation into what happened and it will be interesting to see if Ipswich now make a complaint to the EFL.'
The 49-year-old became a Football League referee in 1996 and officiated in the top-flight two years later. He is also a regular assistant referee in FIFA and UEFA competitions.
He was an assistant referee to Graham Poll in the 2000 FA Cup final between Chelsea and Aston Villa - his first experience as an official in the annual Wembley event.
Drysdale is also a RAF Sergeant veteran and was stationed in Iraq, Libya and Cyprus in his military career.