Investigators "have as yet no evidence or data confirming the theory" of a bomb attack, Hossam Kamal said in a statement.
"The theory of a detonation in the Russian plane is not based on facts," he said. "Egypt is committed to a full and thorough investigation, in order to establish the facts in the eyes of the whole world."
Kamal also defended the security of Egypt's airports, saying they had passed regular audits by Egyptian authorities and international organisations.
Britain and Ireland have temporarily suspended flights to and from the Egyptian Red Sea resort of Sharm el-Sheikh, where the plane took off from on Saturday bound for Saint Petersburg before crashing 23 minutes later, killing all 224 people on board.
The Egyptian branch of the Islamic State group, which is waging a deadly insurgency in the Sinai Peninsula, has claimed it downed the plane.