The £4,500 gem-encrusted silver gilt cup was taken just minutes before the monks were due to hold Mass at Mount Saint Bernard Abbey on Sunday.
The enamelled decorative cup had been used in every service and new monk's ordination since it was struck in 1861.
"It is a big blow," said Abbey prior Father Joseph who also expressed surprise someone was able to remove the cup as it was placed in the sanctuary, on the other side of the barrier from where public worshippers were gathering for the 8am service.
"We're puzzled as to how a person did it," said the prior. "It must have been done very quickly, and they did it without being noticed.
"Whether it was a person who was just very confident and so nobody noticed or it was done in a quick moment, we don't know.
"People were in the church at the time."
A recent valuation described it as a "silver gilt, gem-set chalice" with a "hexafoil base decorated with enamel panels of scenes of The Passion".
The 25cm-high piece of silverware has a stem set with fleur de lis with a tapered bowl "decorated with enamelled panels of angels".
The early Victorian chalice, made in the Gothic style of Augustus Pugin, is thought to have been made by Hardman & Co of Birmingham.
Father Denis, abbey bursar said: "From the transept, you can see the table.
"Perhaps somebody must have observed it there and just hopped over the barrier in St Joseph's Chapel, but who knows.
"It would only be a matter of a few yards to then get to it."
The abbey has 24 monks who keep a guest-house, a herd of 100 dairy cows and maintain their own beehives for honey.
The Cistercian order, who live to a simple code, has been on the site since a monastery was raised there in 1835.