Her name means "a beautiful woman has arrived" and for almost a century the 3,400-year-old bust of the Egyptian Queen Nefertiti has been regarded as a true likeness. Now it seems that in the flesh, she wasn't that good looking after all. The delicately featured bust of the wife of the King Akhenaten has been one of the highlights of Berlin's museum collection ever since it was excavated by German archaeologists and first put on display in 1923. It will shortly take pride of place in the city's recently revamped Neues Museum. But scientific researchers say they have established that her limestone bust appears to have been given a facelift. Call it ancient world Botox.

Using the latest computer tomography techniques developed for medicine, the researchers from Berlin's Imaging Science Institute took a series of scans of the bust and discovered that the sculpture was made up of a limestone core covered in layers of stucco of varying thickness.

Advances in CT technology meant that they were able to probe deeper than a previous scan carried out in 1992. They found that the inner facial cast, which would have been taken directly from the queen's face, differed significantly from the outside of the bust. It had less prominent cheekbones; a slight bump on the ridge of the nose; marked wrinkles around the corner of the mouth and cheeks; and less depth at the corners of the eyelids.

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The cosmetic alterations appeared to have been made by the Egyptian royal sculptor Thutmose, whose studio was dug up by archaeologists at the ancient settlement of Amarna south of Cairo in 1912. The scientists assume that the sculptor would have taken the original plaster mask of the queen's face and used it as a model for the "improved" bust.

"It is possible that the bust of Nefertiti was probably commissioned by King Akhenaten himself to represent her according to his personal perception," said Alexander Huppertz, the director of the institute. "The changes could have been made to make the queen adhere more to the ideals of the time."

The bust is currently a major bone of cultural contention between Egypt and Germany, with Cairo demanding that Berlin hand back the priceless sculpture. Nefertiti's bust was excavated by the German archaeologist Ludwig Borchardt in 1912 and at the time its discovery was hailed as a triumph of Imperial Prussian prowess. Entries in the archaeologist's diaries show that he was beside himself with excitement when he unearthed his find. "Suddenly we have the most alive Egyptian artwork in our hands," he wrote, "You cannot describe it with words. You can only see it."

However documents discovered earlier this year suggest that the Germans tricked the Egyptian authorities out of the sculpture by deliberately covering up its true value before they took it out of the country. Papers found in Germany's Oriental Institute provide an authenticated account of a meeting between Borchardt and an Egyptian official in 1913, shortly before the bust was taken to Germany. The writer of the account recalls how Borchardt, "wanted to save the bust for us".

As a result the German team were reported to have wrapped up Nefertiti and placed it deep in the bottom of a trunk in a dimly lit room in order to fool the authorities. At the same time the Germans allegedly supplied the Egyptians with a deliberately unflattering photograph of the bust and claimed that it was made from gypsum rather than limestone.

The deception paid off and enabled the Germans to smuggle Nefertiti out of Egypt. But the evidence of deception has only served to inflame the row between Cairo and Berlin. The Egyptians have requested that, at the very least, Nefertiti's bust be returned to Egypt on loan to mark the inauguration of a new museum that is scheduled to open near the Pyramids at Giza in 2012. Egypt has threatened never to take part in any future antiquities exhibitions in Germany if Berlin refuses to grant the three-month loan. So far, the Germans have dug in their heels and refused. They say that the bust is too fragile to be allowed to travel.

Dietrich Wilding, the head of Berlin's Egyptian Museum insists that the Nefertiti bust, which attracts more than half a million visitors to the city each year, has attained the kind of global notoriety that would have been less likely had the bust remained in Egypt. "She keeps her separateness and her uniqueness, yet she belongs here," he said.

Germany's Oriental Institute has also been quick to play down suggestions that trickery was used to smuggle out the Nefertiti bust. It argues that the Egyptians should have been more observant. "It is not right to complain about a deal that was reached so long ago," a spokesman said.

Revealed: The queen's hidden face

The differences between the faces (see pictures, above), though slight – creases at the corners of the mouth, far left, a bump on the nose of the stone version – suggest to Dr Alexander Huppertz that someone expressly ordered the adjustments between stone and stucco when royal sculptors immortalised Nefertiti 3,300 years ago.