The incidents date to 2013, when complaints were lodged against the maths teacher at a school in Alexandria, said the ministry's undersecretary Youssef al-Deeb.
"The teacher was fired from the school back then," Deeb told AFP.
The Supreme Administrative Court on Sunday rejected the teacher's appeal against a lower court's decision permanently banning him from teaching, he added.
Elementary schools in Egypt teach children between the ages of six and 12.
Sexual harassment is highly prevalent in Egypt.
United Nations surveys have found that most Egyptian women have been subject to harassment, ranging from catcalling to pinching and groping.
Egyptian authorities have criminalised sexual harassment since 2014 but many women complain that the problem remains rampant.
On Sunday, Education Minister Tarek Shawky told a private TV channel that his ministry "is doing a lot to confront sexual harassment but (the efforts) are not made public for privacy concerns."
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