One of the oldest churches ever to be excavated in Israel was recently discovered at the archaeological site of Tel Shiloh, where the temporary Jewish Temple once stood, in Samaria.This is the only report of the discovery I can find and, as you can see, it seems pretty vague on geography and chronology. The report says that some mosaics and then the church were discovered when a drainage ditch was dug to clear the excavation of rain water.
The church, dating from the fourth century CE, was discovered at the site believed that once housed the Ark of the Covenant of the ancient Israelis. The discovery has created much excitement among Christians.
UPDATE (23 April): Joseph Lauer e-mails to point out that a very similar story circulated back in 2006. It was noted at PaleoJudaica here. It looks as though the new story is just a recycling of the old one.