El-Sissi's remarks came amid days of student demonstrations against the Education Ministry's decision to repeat one of the exams.
He described the leak as "painful" and said "this will not happen again." He spoke at a gathering to break the Ramadan fast attended by public figures in Cairo.
The exams were posted on social networking sites hours before the actual testing time by an anonymous individual who wanted to shine a light on alleged corruption and inefficiency in the ministry.
Scores on the exams directly determine entrance to university faculties. A low score can prevent a student from pursuing medicine or other professions.