While tipping in restaurants in Japan is not done, there is indeed a tipping culture in Japan for a slew of other services though most visitors probably wouldn't encounter it.

Contrary to what's usually said about Japan, with many personalized services tipping is certainly done, but its seen more as a "thank you payment". Sometimes it is given as cash, other times its a gift, and sometimes both. For example, if a Shinto priest comes to bless your land for a groundbreaking ceremony, there isn't necessarily a fixed amount for this service discussed beforehand, but at the end a payment is given, and often it can be quite more substantial than you could ever imagine. And even if there is an agreed amount but you felt the service went beyond it, then an extra amount is often given. The examples are many, especially when it is something that is done more as a individual doing personalized service and/or going well out of their way to accommodate your needs, rather than a company employee just doing their job. A monk doing funeral rites for a family member... a traditional gardener who rescued a cherished tree after being wrecked in a wind storm... even I get this, like when I go cut the otherwise deep weeds around my old neighbor's grave every month. We never agreed on any payment, but none of the descendants live around the area anymore, yet they come to visit the grave a few times a year, and every time they give me some snazzy fruit, a six pack of beer, lots of 'thank yous", and at New Years they include an envelope with a few thousand yen. Indeed, when Japanese "tip" in these instances, they are genuinely thankful when giving and don't see it as some required gesture (like how many tips in places such as the US can feel...)

For a tour guide, it's a bit of a grey area, but the more personalized the tour is, the more understandable that a thank you tip would appreciated by the guide and that it would in fact be culturally normal. So if you are in communication beforehand with a guide for any planning beyond the stated tour, and they are responding well to your queries and offering further advice or suggestions, then you would probably already know before going the level of personalization you are encountering (but as noted above, they may do the obligatory polite refusal upon first offer, but after a equally requisite polite insistence by you they will almost welcomingly take it with a deeply humble thanks). But its not required or expected necessarily, and not doing so will still mean the same service.

But if deciding to tip, do note that giving cash out in the open directly is really awkward. Put any tip in an envelope (don't give coins), and maybe write a brief message of thanks on it (don't write in cursive since even those skilled in English probably can't read it). Any of the 100 yen shops will sell a wide range of gift money envelopes in the stationary section, some are small which need the bills to be folded into quarters, others are the size of the bills themselves, but don't get one thats super elaborate with multi-color ribbons twisted around it (those are for weddings) and definitely don't get one printed with a black and white ribbon (those are for funerals). And if you don't have an envelope, just put the money in a folded piece of paper.