There are many theories regarding Nefertiti's death and burial but, to date, the mummy of this famous queen, her parents, and her children have not been found or formally identified. In 1898, Archeologist Victor Loret found two female mummies inside the tomb of Amenhotep II in KV35 in the Valley of the Kings. These two mummies, named 'The Elder Lady' and 'The Younger Lady', were likely candidates of her remains.

The identity of the queen who wrote the letter is uncertain. She is called Dakhamunzu in the Hittite annals, a possible translation of the Egyptian title Tahemetnesu (The King's Wife). The possible candidates are Nefertiti, Meritaten, and Ankhesenamun. Ankhesenamun once seemed likely since there were no candidates for the throne on the death of her husband, Tutankhamun, whereas Akhenaten had at least two legitimate successors. but this was based on a 27-year reign for the last 18th dynasty pharaoh Horemheb who is now accepted to have had a shorter reign of only 14 years. This makes the deceased Egyptian king appear to be Akhenaten instead rather than Tutankhamun. Furthermore, the phrase regarding marriage to 'one of my subjects' (translated by some as 'servants') is possibly either a reference to the Grand Vizier Ay or a secondary member of the Egyptian royal family line. Since Nefertiti was depicted as powerful as her husband in official monuments smiting Egypt's enemies, she might be the Dakhamunzu in the Amarna correspondence as Nicholas Reeves believes.

The KMT suggested in 2001 that the Elder Lady may be Nefertiti's body. It was argued that the evidence suggests that the mummy is around her mid-thirties or early forties, Nefertiti's guessed age of death. More evidence to support this identification was that the mummy's teeth look like that of a 29- to 38-year-old, Nefertiti's most likely age of death. Also, unfinished busts of Nefertiti appear to resemble the mummy's face, though other suggestions included Ankhesenamun.

In addition to that, there was controversy about both the age and sex of the mummy. On June 12, 2003, Egyptian archaeologist Dr. Zahi Hawass, head of Egypt's Supreme Council for Antiquities, also dismissed the claim, citing insufficient evidence. On August 30, 2003, Reuters further quoted Hawass: "I'm sure that this mummy is not a female", and "Dr Fletcher has broken the rules and therefore, at least until we have reviewed the situation with her university, she must be banned from working in Egypt." On different occasions, Hawass has claimed that the mummy is female and male.

Discovered in 2012, a Regnal Year 16, month 3 of Akhet, day 15 inscription, dated explicitly to Akhenaten's reign, mentions the presence of the "Great Royal Wife, His Beloved, Mistress of the Two Lands, Neferneferuaten Nefertiti". The barely legible five line text "mentions a building project in Amarna" (Egypt's political capital under Akhenaten). The inscription was found in a limestone quarry at Dayr Abū Ḥinnis, just north of Dayr al-Barshā, north of Amarna. The inscription has now been published in a 2014 journal article by Athena Van der Perre who states that the five-line building inscription was found in a limestone quarry at Dayr Abū Ḥinnis. Van der Perre notes that Dayr Abū Ḥinnis is located "on the eastern side of the Nile, about ten kilometers north of Amarna" and records that the building work inscription refers equally to both the ruling king Akhenaten and his great wife Nefertiti under the authority of the king's scribe Penthu. Penthu was presumably the owner of Amarna Tomb 5—where one of his titles given was "first servant of the Aten in the Mansion of Aten in Akhetaten"; due to the rarity of his name and his position as chief priest within the Aten priesthood, it cannot be coincidental—as van der Perre writes—that the same Penthu would have been placed in charge of quarrying stone for the Aten temple. However, as Van der Perre stresses:

During Akhenaten's reign (and perhaps after), Nefertiti enjoyed unprecedented power. By the twelfth year of his reign, there is evidence she may have been elevated to the status of co-regent: equal in status to the pharaoh — as may be depicted on the Coregency Stela.

In 2015, English archaeologist Nicholas Reeves announced that he had discovered evidence in high resolution scans of Tutankhamun's tomb "indications of two previously unknown doorways, one set within a larger partition wall and both seemingly untouched since antiquity...'To the north (there) appears to be signaled a continuation of tomb KV62, and within these uncharted depths an earlier royal interment – that of Nefertiti herself."

Most Egyptologists, among them Kent Weeks and Peter Lacovara, generally dismiss Fletcher's claims as unsubstantiated. They say that ancient mummies are almost impossible to identify as a particular person without DNA. As bodies of Nefertiti's parents or children have never been identified, her conclusive identification is impossible. Any circumstantial evidence, such as hairstyle and arm position, is not reliable enough to pinpoint a single, specific historical person. The cause of damage to the mummy can only be speculated upon, and the alleged revenge is an unsubstantiated theory. Bent arms, contrary to Fletcher's claims, were not reserved to pharaohs; this was also used for other members of the royal family. The wig found near the mummy is of unknown origin, and cannot be conclusively linked to that specific body. Finally, the 18th dynasty was one of the largest and most prosperous dynasties of ancient Egypt. A female royal mummy could be any of a hundred royal wives or daughters from the 18th dynasty's more than 200 years on the throne.