Zahi Hawass also says that steps were being taken to reopen Egypt's famed archaeological sites, which have been closed since unrest seized the country two weeks ago.
During huge anti-government protests on Jan. 28, looters climbed a fire escape and broke into the museum, damaging a number of items, including two mummified skulls from the Late Period.
Originally the skulls were thought to have been attached to mummies, but Hawass said they were being used to test a new CT scanner and were not from the royal mummy collection.
Among the 70 objects damaged was also a statue of King Tutankhamun standing on a panther and a wooden sarcophagus from the New Kingdom period, dating back more than 3,000 years ago.
The museum, which is right next to the massive protests still taking place in downtown Cairo, is now being guarded by the army.
Initially, when the demonstrations began, civilians formed a human chain to protect the building.
The museum is home to the gold mask of King Tut that draws millions of tourists a year, and houses thousands of artifacts spanning the full sweep of Egypt's rich Pharaonic history.
There were fears that the unrest which has gripped the country over the last two weeks could lead to the kind of looting that saw a large part of Iraq's national treasures vanish in 2003 after the fall of Saddam Hussein.
But Hawass said in a BBC interview on Sunday: "The Valley of the Kings is safe, the pyramids are safe, 24 museums are safe, the synagogues and the monasteries and the Muslim monuments are completely safe."
Hawass also asserted that the nearby archaeological digs Saqqara, Memphis and Abu Sir were secure following reports of looting there.