Barnsley FC have made the complaint following an alleged incident over the weekend
Following Fleetwood's 4-2 loss to Barnsley an incident allegedly took place between both the clubs managers, Daniel Stendel and Joey Barton.
Barnsley have mande an official complaint to the English Football League and Football Association.
The club confirmed that manager Stendel suffered facial injuries but is 'OK' after the alleged incidents.
Police stopped Barton from leaving Barnsley's stadium as they investigated the alleged assault.
Footage showed the former England and Manchester City footballer being driven from Oakwell Stadium before an officer stood in front of the vehicle to stop it.
It's understood South Yorkshire Police have spoken with Barton, and will speak to him again later in the week as part of a voluntary interview.
Barnsley said in a statement:
"The club can confirm there was an alleged incident in the tunnel area that took place following the conclusion of today's match, which South Yorkshire police are currently investigating.
''The club is assisting the police with its enquiries and, as a result, we are not in a position to make any further comment at this time."
Fleetwood Town have also issued a short statement that said: ''Fleetwood Town have been made aware of an alleged incident following Saturday’s game against Barnsley.
''We are currently establishing the facts and will not make any further comment at this time.''