A more advanced scan will be conducted later this month to ascertain whether the empty spaces are in fact chambers.
A British Egyptologist believes Nefertiti was buried there. She ruled in the 14th Century BC, and may have been Tutankhamun`s mother.
His tomb was discovered in 1922 by British archaeologist Howard Carter.
Mystery design
Announcing the results of November`s scans on Thursday, Antiquities Minister Mamdouh el-Damaty said they had revealed the presence of two empty spaces behind two walls of the burial chamber.
"We can say more than 90% that the chambers are there. But I never start the next step until I`m 100%." [The scans point to] different things behind the walls, different material that could be metal, could be organic."
He added: "For Egypt it is a very big discovery, could be discovery of the century." "It is very important for the Egyptian history and for all over the world."
The British Egyptologist Dr Nicholas Reeves believes the remains of Tutankhamun, who died 3,000 years ago
aged 19, may have been rushed into an outer chamber of what was originally Nefertiti`s tomb.
He posited in early 2015 that Nefertiti may have been buried there too after examining scans of the tomb, near the site of the original Valley of the Kings in Luxor.
Tutankhamun`s tomb was the most intact ever discovered in Egypt. Close to 2,000 objects were found inside.
But its layout has been a puzzle for some time - in particular, why it was smaller than those of other pharaohs` tombs.
Dr Reeves believes there are clues in the design of the tomb that indicate it was intended to store the remains of a queen. His theory has yet to be peer-reviewed and leading Egyptologists have urged caution over the conclusion.
Some believe that Nefertiti`s mummy was discovered in 1898 and is now in the Egyptian Museum in Cairo.
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