Newcastle midfielder Emre is one of five players facing Fifa individual disciplinary proceedings. It follows completion of Fifa's initial investigations into the post-match violence at Turkey's World Cup play-off against Switzerland
Emre, former Aston Villa defender Alpay and Swiss defender Benjamin Huggel all face individual action.
The Turkish FA, Turkey assistant manager Mehmet Ozdilek and Swiss physio Stephan Mayer also face proceedings.
Fifa has launched what is claimed to be the biggest disciplinary inquiry in its history into the violent scenes which marred the end of the match in Istanbul on 16 November.
The Swiss players were pelted with missiles at the final whistle and Huggel was seen to kick a member of the Turkish coaching staff as he ran off.
Swiss defender Stephane Grichting was taken to hospital and needed a catheter inserted after being kicked in the stomach during a free-for-all in the tunnel.
A Fifa statement said: "The results of the investigation will determine whether additional individual proceedings are brought against those concerned, or whether further hearing and more evidence are necessary."