The question included the statement: "In the animal kingdom, a sheep cannot be king."
Critics often accuse Muslim Brotherhood members of acting like sheep by following the orders of the group's leader, Ahram Online said.
But English teacher Ihab el-Islamboly told Ahram Online he did not intend to insult the president and the quote is part of the curriculum.
"What part of this quote has anything to do with the president or politics?" el-Islamboly asked.
The incident comes after a deputy education minister in the Kafr el-Sheik area of Egypt ordered a punishment for a teacher Saturday.
The teacher included a question involving an imaginary dialogue between ousted President Hosni Mubarak and Morsi, Ahram Online said.