The two mummies, complete with elaborately decorated stone coffins, were found in Kiev's Pechersk Lavra.
Also known as the Monastery of the Caves, the historic Orthodox Christian monastery revealed its hidden treasures during an audit.
The artefacts were recovered after spending many years hidden in a museum archive with the Egyptian artefacts believed to date as far back as the 11th century BC.
The search also uncovered a rare mummified 161-centimetre crocodile, believed to be from the Temple of Horus and Sobek at Kom Ombo, as well as several canopies - funerary vessels used to store internal organs.
Mykola Tarasenko, doctor of historical sciences, said: "This mummy comes from the Temple of Horus and Sobek at Kom Ombo.
"Crocodiles were considered to be sacred to Sobek. I know only of two or three crocodiles this big in Italy. And there's one in the British Museum."
The 3,000-year-old mummy of a woman named Menat, a singer in the temple of Amon in Ancient Egypt was discovered inside one of the stone coffins, or sarcophagi.
Experts say the finding is unusual due to Menat's hands being positioned in a style commonly used in male burials.
According to historians, her head was accidentally severed from her body during frequent transportations.
The second mummy was of a male, whose identity remains a mystery.
However, clues from his coffin suggest he was a member of Egypt's elite, with the burial style customary of the 11th and 10th centuries BC in Thebes, the capital of ancient Egypt.
Yevhen Nyschuk, minister of culture of Ukraine, said: "For Ukraine, these kinds of findings are a testament to the fact that relics of other world civilisations are stored on our territory.
"This gives the possibility for a whole school of egyptology to develop.
"The finds will be exhibited to a wide audience. Soon we'll organise either on this complex's territory, or in another museum, a special hall designed with all the conditions in mind to preserve these artefacts."
It is believed the mummies came to the Ukraine in the second half of the nineteenth century.
According to the Ukrainian Culture Ministry, the mummies were stored initially at the Church Archeological Museum, before being moved to the Museum of Atheism - which at the time was housed by Kyiv Pechersk Lavra.
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