Byrne was briefly a 16th Ospreys player on the pitch during his team’s 17-12 Heineken Cup victory over Leicester that secured a quarter-final place.
He had gone off with a bloodied toe, to be replaced by centre Sonny Parker, but Byrne then went back on without any team-mate leaving the field for almost a minute.
Leicester lodged an official complaint with the tournament organisers, European Rugby Cup, whose disciplinary officer Roger O’Connor has now lodged misconduct complaints.
Byrne and the Ospreys will face a disciplinary hearing in Dublin tomorrow.
The developments, another embarrassment for tournament organisers are potentially bad news for Wales coach Warren Gatland just 10 days before his team’s Six Nations opener against England at Twickenham.
Lions full-back Byrne has recently returned to fitness after missing the entire autumn Test series through injury.
But there is now the possibility he could be banned, while the Ospreys will be left sweating on a possible fine, or worse — a points deduction.
They booked a last-eight place as one of two best pool runners-up, finishing behind Clermont Auvergne, but two points above Leicester.
In a statement, ERC said: “ERC disciplinary officer Roger O’Connor has now completed his investigation into the allegation the Ospreys had 16 players on the pitch during the second half of the Heineken Cup match between the Ospreys and Leicester.
“As part of his investigation, he reviewed statements from the Ospreys, Leicester and the match officials, and also reviewed footage of the incident.
“Following his investigation, the disciplinary officer has made misconduct complaints against Ospreys full-back Lee Byrne and the Ospreys club.
“The independent disciplinary officer appointed to hear the case in Dublin on Friday will be chaired by Pat Barriscale (Ireland), and also includes Jean-Noel Cournaud (France) and Mark McParland (Ireland).”
Chaos ensued at the Liberty Stadium when Byrne rejoined the action. Referee Alan Lewis was seemingly unaware he returned, and berated an Ospreys touchline official.
Lewis should have awarded Leicester a penalty once Byrne’s reappearance became evident, but it is understood the official might have been told by an unnamed Ospreys player that Leicester also had 16 on the field.
Leicester moved quickly after the final whistle, with club chief executive Peter Wheeler and chairman Peter Tom both confirming a complaint was made within an hour of the finish.
Tom was also due to write directly to ERC chairman Jean-Pierre Lux, while the Tigers have hired a team of specialist sports lawyers to head up their protest.
The 16th-player episode comes with dust only just settling on last season’s big Heineken Cup controversy.
That was the Bloodgate episode during a quarter-final between Harlequins and Leinster, when Quins wing Tom Williams was ordered to fake a blood injury in an attempt to get goalkicker Nick Evans back on the field during a game subsequently Quins lost 6-5.
After a lengthy ERC investigation, Williams, former Quins rugby director Dean Richards and ex-club physiotherapist Steph Brennan were all banned for varying periods. Richards and Brennan have both left Quins, while Williams is now playing for them again after completing his suspension.