The France defender was caught in the face by the home side's Pierre Webo who was booked after the incident.
Koscielny received treatment on the pitch but was eventually replaced by Carl Jenkinson as blood streamed down his face, before receiving stitches in the dressing room and being taken to hospital.
Off you go: Koscielny was replaced by Carl Jenkinson as Arsenal were hit by another injury blow
Wenger was less than impressed by the challenge. He said: 'Laurent Koscielny has opened very deeply the skull and we had to take him to hospital.
'I was not happy with the kick because I feel always that you can ease a bit off. Only the player in the end will know what he did.
'We are concerned because we had to send him to hospital to see if he has not broken a bone. We are waiting for him to come back now, for information to find out if he can fly home with us.'
Goalkeeper Wojciech Szczesny was also on the receiving end of a late challenge from Moussa Sow as he dived to make a save in the second half.
The Pole was another who needed treatment on face and neck injuries but was able to continue as Arsenal won 3-0 thanks to Kieran Gibbs, Aaron Ramsey and an Olivier Giroud penalty.
Low blow: Wojciech Szczesny took the full brunt of Moussa Sow's boot during Arsenal's game in Turkey
Arsenal already have a length injury list which was exacerbated by the news that Alex Oclade-Chamberlain will be sidelined until November.
The midfielder said he hopes to be 'back playing in three months' following his knee injury, but he is set to miss crucial games for club and country in the meantime.
The 20-year-old, who has become a regular member of Roy Hodgson's England squad, limped out of the Gunners' 3-1 home defeat by Aston Villa on the opening day of the new Premier League season.
Thomas Vermaelen, Mikel Arteta and Abou Diaby were also missing as Arsenal took a massive step towards reaching the lucrative group stages of Europe's premier competition.
Gibbs also suffered a cut to the head against Villa but recovered in time to take his place in the line-up on Wednesday.