In an interview with Przeglad Sportowy, Maciej Szczesny accused Gunners boss Wenger of using his son as a scapegoat for the club's poor season.
Maciej Szczesny's made the comments after Wojciech was dropped for the second leg of Arsenal's Champions League tie with Bayern Munich last week, with Wenger claiming the 22-year-old had been "mentally affected" by the number of games played.
The Poland international was then put on the bench for the Premier League win at Swansea, where Lukasz Fabianski kept a second consecutive clean sheet.
Although currently on international duty, Wojciech Szczesny responded to his father's outburst in a statement posted on Arsenal's official website.
"I would like to apologise for the comments made by my father which have been used by both Polish and English media," he said.
"I'd like to make it clear that those were the views and opinions of my father and not mine, and although I respect his views I cannot accept them as I find them disrespectful to the club I truly love.
"I have been at Arsenal Football Club for seven years now and I have always shown my full respect to the club, Arsene Wenger, all the coaching staff, my team-mates and the fans.
"I've always felt that I received great support from the manager and the fans and I am fully focused on getting back to my best.
"I am proud to be a part of Arsenal and I see my future at this great club."