Mohammad Musa was scheduled for arraignment Tuesday on misdemeanor charges of assault and harassment.
The policeman and his father were kneeling in prayer Friday when the older man was pushed. The policeman was punched in the face when he commented on the shoving.
The lieutenant reportedly was wearing a shirt with an NYPD logo.
But the district attorney's office said it had no evidence of anti-police sentiment.
A relative of the defendant said crowded conditions led to a misunderstanding. The incident occurred during Ramadan prayers at the Noor Al-Islam Center.