The disputed exhibit is housed in a gallery called Asian Crossroads. Entitled "the rise and spread of world religions", the panel mentions Christianity, Islam, Hinduism and Buddhism.
A spokeswoman for the Ashmolean explained that it did not state "all world religions".
The four religions listed had "tended to spread - through conquest, proselytism or cultural osmosis - in a way different from the manner in which the historic Jewish diaspora occurred.
"The history of the Jews would require a text panel or display of its own… The other point is that the four named religions spread generally more freely than Judaism among other ethnic groups, thus influencing other regional cultures more readily."
She said that after consulting various scholars about changing the wording - including leading Oxford University's Professor Martin Goodman, a Jewish expert on antiquity, the museum had been "advised that any such change would be inappropriate to the historical context of the panel", which covered the first millennium AD.
But Dr Pinto-Duschinsky said: "Judaism did spread after 300 CE. There is a reference to the Cairo Genizah elsewhere in the same gallery. Moreover, Judaism is not alone in having been established before 300 CE. An earlier date of establishment has not prevented the inclusion of other religions, so why exclude Judaism?"
He said he welcomed the idea of a new Judaism trail.
The museum said the trail will be developed with Professor Goodman, linking Jewish items from Roman and medieval times.
Earlier this year, Sunday Times columnist Dominic Lawson suggested the Ashmolean contained "remarkably little" about Judaism, while noting the funding of a new gallery by the Saudi royal family. The Ashmolean, part of Oxford University, said its holdings were "in no way influenced by any donor".
