Researchers including Stephen Buckley and Joann Fletcher from the University of York in the UK used radiocarbon dating, anthropology, palaeopathology, genetics and chemical analysis to identify the remains.
They conclude that "the most likely scenario is that the mummified knees truly belong to Queen Nefertari".
As the favourite wife of the pharaoh Ramses II, Nefertari was provided with a beautifully decorated tomb in the Valley of the Queens to which Fletcher was recently given access.
This included a pair of mummified legs which could have been part of a later interment as was often the case in other tombs in the region.
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However, as the legs had never been scientifically studied, it was decided to undertake the recent study to find out if the legs could actually represent all that remained of one of Egypt's most legendary queens.
The study showed that the legs are those of an adult woman of about 40 years of age.
"The evidence we've been able to gather about Nefertari's remains not only complements the research we've been doing on the queen and her tomb but really does allow us to add another piece to the jigsaw of what is actually known about Egyptian mummification," Fletcher said.
The study was published in the journal Plos One.