The ministry charged that Mohamed Kamal headed the military wing of the movement of ousted president Mohamed Morsi, although the group has always denied having one.
It said that he and fellow Brotherhood member Yasser Shehata were killed in a firefight when police raided their hideout in the southeast of the capital late on Monday.
The ministry alleged that Kamal had founded the Brotherhood's military wing after the army's overthrow of Morsi in 2013.
Signup to our newsletter and follow us on Facebook and Twitter!
It said he had been given two life sentences in absentia on charges of forming an armed group and involvement in a bombing near a police station in Assiut in southern Egypt.
It said he was also wanted on suspicion of involvement in the murder of prosecutor general Hisham Barakat in a June 2015 car bombing and the attempted murder of leading Muslim cleric Ali Gomaa in August.
The Brotherhood and its supporters have been subjected to a deadly crackdown since Morsi's ouster but it denied taking up arms in response.
Hundreds of soldiers and policemen have been killed in attacks since 2013 but most have been claimed by jihadists who have pledged loyalty to the Islamic State group.