Her mummy may have been hidden in the tomb for safekeeping after her death because her stepson and successor, Tuthmosis III, tried to obliterate her memory.
Donald Ryan, an Egyptologist who rediscovered the tomb in 1989, said on an Internet discussion board this month that there were many possibilities for the identities of the two female mummies found in the tomb, known as KV 60.
"Zahi Hawass recently has taken some major steps to address these questions. Both of the KV 60 mummies are in Cairo now and are being examined in various clever ways that very well might shed light on these questions," he added.
In an undated article on his Web site, Hawass cast doubt on the theory that the KV-60 mummy with the folded right arm was that of Hatshepsut.
"I do not believe this mummy is Hatshepsut. She has a very large, fat body with huge pendulous breasts, and the position of her arm is not convincing evidence of royalty," he wrote.
He was more optimistic about the mummy found in the wet-nurse's coffin and traditionally identified as the nurse's. That mummy is stored away in the Egyptian Museum in Cairo.
"The body of the mummy now in KV 60 with its huge breasts may be the wetnurse, the original occupant of the coffin ... The mummy on the third floor at the Egyptian Museum in Cairo could be the mummy of Hatshepsut," Hawass wrote.