Such documents represent an additional security risk for European states grappling with a large influx of refugees from countries including Syria and Iraq because they are harder to identify than outright fakes.
One diplomat said the list contained serial numbers of thousands of genuine blank passports that were held in government offices in parts of Syria and Iraq which have since been captured by armed groups including Islamic State.
The diplomat said there were around 5,000 missing Syrian passports from Raqqa and Deir al-Zor provinces on the list and 10,000 Iraqi ones from areas of Anbar, Nineveh and Tikrit.
The U.S. government has warned that Islamic State has the ability to create fake Syrian passports, in a report that appears to draw on the same information described by the diplomats.
The passport watch list was first shared between several European Union states in the summer, when tens of thousands of refugees started arriving in Europe, and has been updated several times since, diplomats said.
The debate on how to deal with the influx of refugees to Europe has become more politically charged after deadly attacks in Paris that stoked fears Islamic State militants could exploit the migrant crisis to send extremists to Europe.
A Syrian passport was found near the dead body of one of the attackers and his fingerprints matched those of a person registered as arriving in Greece in October, although it has not been confirmed that he was the man named in the passport.
FBI Director James Comey told a U.S. Senate committee on Wednesday that the intelligence community is concerned Islamic State has "the ability, the capability to manufacture fraudulent passports, which is a concern in any setting".
(Reporting by Sylvia Westall; Editing by Catherine Evans)