The French defender took a kick to the skull from Pierre Webo while stooping to clear a ball in the Champions League qualifying play-off at the Sukru Saracoglu Stadium.
Gunners manager Arsene Wenger confirmed that the defender was taken to hospital to assess the damage and is awaiting an update on the severity of the problem.
"Laurent Koscielny's [injury] has opened very deeply the skull and we had to take him to hospital," he told the media after the game. "I was not happy with the kick because I feel always that you can ease a bit off.
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Despite securing an important victory in Turkey, Wenger was left angered by the Koscielny incident.
"We faced a lot of challenges on Saturday [against Aston Villa] and again [against Fenerbahce]. That is part of the intensity of the game. Of course, there was so much at stake you can understand that," he continued.
"This special challenge, I don't know really what to think about it. When I saw it, I was angry but I don't know if the player can explain to you exactly what he did."
Wenger also revealed confirmed that Alex Oxlade-Chamberlain could face up to 12 weeks out of action with a knee injury, having initially spoken of a timescale of at least six weeks. The Arsenal boss had been swiftly corrected by the midfielder's Twitter post, confirming Goal's exclusive revelation of the length of his absence.
"It could be a bit longer than what I said," the Frenchman admitted. "There is no surgery – it will be between six and 12 weeks."