Diaby was ruled out of action for three weeks with a thigh injury in a 2-1 defeat by Chelsea in the Premier League 12 days ago.
It followed Wenger's criticism at Deschamps decision to field Diaby in both of France's World Cup qualifiers just a few days apart last month.
But Wenger insists: "I have no problem with Didier Deschamps.
"It was not even my opinion. It was the opinion of my MEDICAL staff that Diaby was not in the position to cope with playing for both Arsenal and France at the moment because when you have been out for a year you have been out for a year.
"I have spoken to him and told him that."
Deschamps was furious with Wenger last week when he named his squad for Friday's friendly against Japan and the World Cup qualifier with Spain next Tuesday.
He said: "I want to remind him that I am the only one to decide who will be picked and how long those who are picked will play. There is only one to decide and it's me."