PH Niseko has an onsen as well as some rooms with rotenburo (in room hot spring bath), PH Kyoto has a few rooms with onsen bath as well IIRC. Under IHG the Indigo Hakone and IC Beppu have onsen (Indigo every room, IC not all rooms though). IC and CP Appi Kogen have them too.

Of course these are only a few while there are thousands of Japanese Ryokan with onsen and someone mentioned the Hoshino resorts and also Tsugaru group (focus on Hokkaido) though some properties in those portfolios can be great while others can be meh, YMMV. Definitely interesting, let's see what they will come up with.

I think many people (especially tourists, I include myself there) may be a bit intimidated by the full blown, top end Japanese ryokans as there can be lots of rules to be followed that are not necessarily known to foreigners, plus you better have a very well filled wallet .
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