Uzumasa-no-Kijima Jinja is ostensibly a Shinto Shrine and functions as one today. But the hereditary priest and his family that have run the shrine for countless generations hold a "secret" theory that it was originally a Christian church.

Whether they are making this up, or sincerely believe it but are deluded, or are 100% correct, I could not say.

Uzumasa-no-Kijima Jinja does have some unusual features. Firstly, it has a Torii (Shinto gate) that is decidedly different from most "normal" torii. The standard Torii has two pillars, but as you can see, this one has three.

(Scroll down a bit for some pics of the three-pillared shrine):
[link to home.s01.itscom.net]

Gabi Greves, who conducts exhaustive analyses of various shrines, states rather laconically:
Some sources state that this was a secret symbol of the underground Christians for the Holy Trinity. The [Shrine personnel] explain the three pillars represent
faith, hope and charity.

gotta admit that last part sounds pretty darn Christian...

Couldn't find much about the so-called "Well of Israel," But I did find out that this shrine is associated with the Hata Clan, who also are associated with several other nearby shrines. One of them conducts an unusual and very un-Shinto-ish ritual where participants enter some "holy purifying water" to "wash away their sins." The parallels with baptism are obvious although perhaps not utterly decisive.

Yet another Hata-Clan-Associated Shinto Shrine called Ohsake Jinja is in the same vicinity and this is what the author of "Lost Identity" writes about it:

[Visiting the Shrine, I said to the priest] "Excuse me...I've been told that about 1400 years ago, people from Assyria came to Japan bringing with them ancient Christianity and that they built a church right here. Do you know anything about that?"

I fully expected to receive a cold response and be
ushered out with, "Don't be ridiculous! There was no such thing!" But to the contrary, the priest said, "What an interesting thing you say. Actually, this shrine is closely related to the "Hata" people, and to be honest with you, it is really an unusual shrine." He continued to share with me the history of the shrine and the "strange" objects that were enshrined there, including the items that were worshipped by the Hata people....

...The priest continued, "The number 12 is used very often
here at this shrine. You give 12 offerings, and there are 12 stones, and other such things having to do with 12." I was thinking as I listened to him that the ancient Israelites set up 12 pillars because they were made up of 12 tribes,
and the number 12 appeared in numerous other contexts as well, including the number of disciples Jesus had. In fact, the number "12" in the Bible was a symbol for "redemption" and "salvation". Thus, 12 was also important to the followers of Keikyo and other eastern Christian sects.

The priest also said that even though the Ohsake Jinja
enshirined Hatano Kawakatsu as a [diety], originally, [Hatano Kawakatsu had been a human being of the Hata clan, and it was really] that which Hatano Kawakatsu had worshipped that was enshrined. So what was it that he had worshipped?"

What indeed?