Sir Elton bought the piece at Sotheby's in London four years ago for about pounds 8,000, believing its provenance to be completely sound.
However, late last year the auction house contacted him to ask for the piece back when it emerged that the sale may not have been lawful. There is no suggestion that either party knew there was a problem with the piece, but the need for its return has resulted in Sotheby's conducting a world- wide search to find a replacement for him.
The singer bought the antiquity at auction on 8 December 1994. It is described in the sale catalogue as Lot 133: "A fragment from a Roman marble sarcophagus, circa 3rd- century AD."
A brief description continues: "With the figure of a horseman, a slain figure below, another figure on the corner, the scene would appear to represent an Amazonomachy [an Amazon battle]."
Measuring 59cm by 35.9cm (231/4 in by 141/8 in), the catalogue estimated its value at between pounds 6,000-pounds 8,000.
It is understood that Sir Elton, a great collector of fine art, still displays the fragment in the drawing room of his home in Old Windsor Berkshire, and regards it as one of his favourite pieces. His representatives are co-operating fully with Sotheby's officials who, in turn, are searching for a similar, replacement piece.
One dealer said a full refund had been offered by Sotheby's, but it was turned down in the hope that a similarly fine piece could be found elsewhere. "He got more pleasure from the artefact than he ever could from the return of the money," the dealer said.
"The worst part about it was that last year was a terrible one for Sir Elton, with the loss of his friends Princess Diana and Gianni Versace. The last thing he needed was to have something else taken away from him."
Chris Proudlove, a spokes- man for Sotheby's confirmed the fragment had been stolen.
"It will be returned to its owner when a replacement can be found," he said. "We are working with Elton John's organisation to find a replacement as soon as possible."
Mr Proudlove declined to give details of the sale price, or a fuller description of the piece on the grounds of client confidentiality.
It is not known from whom the piece was stolen.