The 3D imaging showed that the kestrel was force-fed its last meal - a mouse - suggesting it was kept in captivity.
This is the first evidence to point to mass breeding of raptors as offerings to gods, researchers said.
Researchers from the American University in Cairo, Stellenbosch University in South Africa and the Stellenbosch Institute for Advanced Studies said the findings have implications for use of birds of prey in falconry for hunting.
Ancient Egyptians believed in many gods and associated different animals with them; raptors like kestrels were connected to the sun god Re.
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"The idea of birds of prey being bred to the extent of being kept and force-fed is new," said Dr Salima Ikram, Professor of Egyptology at the American University in Cairo and lead author of the study.
"Until now, the sheer number of raptor mummies had been a mystery - did they catch or trap them and kill them, raid nests, or find them dead? Our results explain why they had so many: we now think it was because of active breeding," Ikram said.
The researchers carried out a virtual autopsy on a bird mummy from Iziko Museums of South Africa in Cape Town. The bird mummy, SACHM 2575, was scanned using CT imaging and the team created 3D images of the bird.
Based on morphology, limb measurements and beak shape, they established it was a European kestrel (Falco tinnunculus).
They found the tail of a young house mouse which appears to have caused the kestrel to choke to death.
Looking further into the gizzard and stomach, they found other mouse fragments, including 27 loose teeth, suggesting that the kestrel had eaten more than one mouse earlier in the day. They also found parts of a small sparrow.
"This was one of the most entertaining and exciting bits of research to do - when we saw how much the kestrel ate and how it choked, we suddenly had an idea about how the ancient Egyptians managed to mummify so many raptor and the implications about wild animal husbandry and the possibility of falconry being practiced in ancient Egypt," said Ikram.