If you're in the Karuizawa area, this is a nice unexpected detour. Catch the local train from Karuizawa to Nakakaruizawa. It's only a 17 min walk from Nakakaruizawa station along the main road and then turn left up a shared road that isn't marked.There isn't any signage to get there. Once at the top, it is quite a marvel to look at. Inside it's quite small but has a flowing stream and lush green plants. Note that you won't be able to take photos inside the church.
after the church you may want to walk further up the main road to get to the terraces where there are some quaint shops overlooking the river. It's only a further 5 min walk from the stone church.
Overall a nice half day detour if you're in Karuizawa.