Koeman, reading from a prepared statement, said: "Obviously I am very disappointed by this situation regarding Wayne Rooney. We have spoken on Tuesday and the chairman Bill Kenwright spoke also to Wayne about this situation. In line with any disciplinary matter this will be dealt with internally at an appropriate time and that is all I have to say about the case of Wayne Rooney."
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Koeman last month spoke of the positive influence Rooney, who has scored twice in seven appearances since returning to his boyhood club, has had in the dressing room.
Asked whether the situation had affected the player and whether it would impact on the manager's selection, Koeman added: "He will play this Saturday (against Tottenham). If I see that Wayne is not in a physical or mental condition to play then he won't play."
Koeman's other issue over the international break was the collapse of Ross Barkley's £35million transfer to Chelsea.
The 23-year-old, currently sidelined by a grade three hamstring tear likely to keep him out until November at the earliest, pulled out of the move at the last minute on deadline day despite travelling to London.
Barkley is in the final year of his contract, having rejected the offer of a new deal from Everton, but Koeman refused to say his Toffees career was over.
"Ross also came to see me on Tuesday and he explained to me why he turned down (the chance) to go to Chelsea," said the manager. "That is a private talk with Ross and I am not the right man to explain to you about his decision or the reason for that decision.
"He was open to make a move to another club and from what I heard from the board, there was an agreement between Chelsea and Everton. But finally the decision was by the player and that is what happened at that time."
Asked whether his Everton career was over Koeman added: "No, he is still an Everton player and he has a contract until the end of this season.
"At this time he is injured and it will take another two to two-and-a-half months until he is available. I don't have to take a decision, I can wait to see what happens and then we will see what the decision will be at that time."
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