Among the stolen antiquities was a statue of the daughter of Pharaoh Akhenaten, who ruled during the 18th dynasty. Archaeologist Monica Hanna described it as a "masterpiece". Other looted items included gold and bronze Greco-Roman coins, pottery and bronze-detailed sculptures of animals sacred to Thoth, a deity often represented with the head of an ibis or a baboon.
The museum's ticket agent was killed during the storming of the building, according to the Antiquities Ministry.
Under the threat of sniper fire on Saturday, Hanna and a local security official were able to salvage five ancient Egyptian sarcophagi, two mummies and several dozen other items left behind by the thieves.
The museum was a testament to the Amarna Period, named after its location in southern Egypt that was once the royal residence of Nefertiti. The area is located on the banks of the Nile River in the province of Minya, some 190 miles (300 kilometers) south of Cairo.
When Hanna asked a group of teenagers wielding guns to stop destroying the artifacts that remained, they said they were getting back at the government for killing people in Cairo, she said.
"I told them that this is property of the Egyptian people and you are destroying it," she said in an interview Monday. "They were apparently upset with me because I am not veiled."
After managing to chase them away, a group of men began opening fire to try to force her and the security official to leave. She said the men were apparently also in charge of the boys, who had burned one mummy completely and partially burned another, while pushing around a half-ton statue from the Old Kingdom of the third millennium B.C.
"We were working and lowering our heads so they do not fire on us. There were snipers on rooftops," she said.
The two were able to salvage some 40 artifacts and thousands of broken pieces that Hanna said will take archaeologists years to put back together. The Egypt Heritage Task Force, a group of Egyptian archaeologists who use social media to try to raise awareness about illegal digging for artifacts and looting, said 1,050 pieces were stolen from the museum.
The head of museums for the Antiquities Ministry, Ahmed Sharaf, said two statues were returned Monday. He told The Associated Press that police and ministry officials will not press charges or arrest anyone who comes forward with looted items and that a small financial reward is available for returned artifacts.
He said that until now, police have been unable to secure the museum. He accused members of ousted President Mohammed Morsi's Muslim Brotherhood, who have been spearheading protests against the government, of being behind the looting and attacks on the nearby police station.
Hanna said the looting was more likely carried out by heavily armed gangs of thieves who took advantage of the lawlessness to target the museum.
The chaos erupted Wednesday when security forces in Cairo, authorized by the new military-backed government, cleared out two Islamist-led sit-ins demanding Morsi be reinstated, igniting violence that has killed more than 1,000 people.
The Great Pyramids west of Cairo and the Egyptian museum in the heart of the city were closed during the country's bloodiest day last week. At least 30 tanks line the streets outside Egypt's main museum in Cairo.
Some looting occurred during the 18-day uprising in early 2011 against autocratic President Hosni Mubarak. More than 50 items were stolen from the Cairo museum, but Sharaf said around half have been recovered.
Never, though, was the looting then or at any other time since on the scale seen last week, according to archaeologists and ministry officials.
In the past two years of instability since Mubarak's ouster, illegal digs have multiplied and illegal construction has encroached on ancient, largely unexplored pyramids.
Also threatening sites is the view held by some hard-line religious allies of Morsi who view Egypt's ancient history as pagan.
The Malawi Museum was in many ways a tribute to the heritage of Minya and home to chests, coffins, masks and hematite stone with Hieroglyphic inscriptions used for measuring. The looters also made away with sculptures associated with the deity Thoth, who ironically, is known as an arbitrator of disputes.