Egypt's top prosecutor has referred three Germans to criminal court on charges of smuggling and damaging antiquities and six Egyptians for acting as their accessories.
Hisham Barakat said authorities issued arrest warrants for the alleged German thieves, who fled to their country after the incident.
He said authorities would communicate with Germany to restore the pieces they say were taken last April under the pretext of use for research.
The Egyptian defendants were already in detention.
Barakat said the Germans, along with their Egyptian guides, entered the famed pyramids of Giza with permits to visit, but not excavate, and left with samples of stone from the ramparts of two tombs and the burial room of King Khufu.
Egyptian archaeologist Monica Hanna said the German researchers wanted to use the samples to prove their hypothesis in a documentary they later filmed, which said that the pyramids were built by a people that pre-dated the ancient Egyptians.
The online documentary, removed in the wake of the controversy, showed one researcher inside the inner chambers of the Khufu pyramid, taking samples from the king's cartouche.
Egypt has experienced a security vacuum since its 2011 uprising. Thousands of artifacts have been stolen.
Meanwhile, Spanish archeologists have unearthed a 3600-year-old mummy in the ancient city of Luxor, Egypt's Antiquities Minister says.
In a statement, Mohammed Ibrahim said the rare find in a preserved wooden sarcophagus dates back to 1600BC, when the Pharaonic 17th Dynasty reigned.
He said the mummy appeared to belong to a high official. The sarcophagus was engraved with hieroglyphs and decorated with inscriptions of birds' feathers.
The exact identity of the well-preserved mummy would now be studied, Ibrahim said, adding that it was discovered by a Spanish mission in collaboration with the Egyptian antiquities ministry.
Antiquities department head Ali Al-Asfar said the two-metre sarcophagus still bore its original colouring and writings.