The London side conceded both goals in Saturday's 2-2 draw against Southampton via headers from set pieces and Wenger said he had discussed with his team what had gone wrong at the back.
"We spoke about this today and we are concerned that we are not as strong in the air as we used to be," he said.
"We have to work on this and I do not see it is difficult."
Wenger will again be without injured England centre back Sol Campbell against Panathinaikos.
Wenger said Campbell would also miss the team's next Premier League match at Crystal Palace and Brazilian midfielder Gilberto will be out for at least three months with a back injury.
Arsenal are second in Group E with five points, one adrift of PSV Eindhoven who host bottom side Rosenborg Trondheim. Panathinaikos are third on four points.
"A victory tomorrow gives us an 80 percent chance to qualify," the Frenchman told a news conference on Monday. "So you can imagine how big a game this is for us."
The English champions, who have never lost to Greek opponents on home soil, saw their 2-1 lead in Athens two weeks ago disappear in the last 10 minutes after an Emmanuel Olisadebe goal.
Wenger said he expected another tough game on Tuesday.
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Arsenal's captain Patrick Vieira said: "They are a physically strong side who have two strikers up front who can score goals and the midfield will be packed.
"It will be difficult for us to find space."
Arsenal's 49-game unbeaten league run ended with a defeat at Manchester United on October 24 and Wenger said on Saturday his side would have suffered a confidence crisis if they had lost to Southampton.
"Our confidence is still really high. If we win the game we'll be in a comfortable zone," said Vieira.
