Vending machines also won't take the ¥1, ¥5, or ¥10 coins...
Luckily the conbini shops have machines that do take them and allow you to dump a whole handful of change in at once and will give change back in the minimal configuration. So my recommendation in Japan is when you buy something at the conbini, dump all of your loose change into the machine, then pay the rest with a ¥1,000 notes and you will get the minimal number of coins back.
Oh, and you can throw the ¥5 coins into the local shrine for good luck. :-D
My personal Japan Trip Lifehack was to dump all the coins into the nearest transit card charge machine. The PASMO machines are the most flexible, there's a button for "charge in 10 yen increments", and the only thing those don't take are 1 and 5 yen coins. Suica and Hayakaken[0] machines were a bit pickier, you had to have at least 100 yen of change. Whatever the heck they used in Osaka was the pickiest - it was either 500 yen increments or it didn't take small coins, I don't remember which, but I remember having to hold all my change until I got back to Tokyo.
My personal Japan Trip Lifehack is to pay for all the small awkwardly numbered purchases (kombinis, supermarkets, fast food etc) with your Suica/Pasmo. This eliminates virtually all Y1/5 coins, since "proper" restaurants, transport, attractions etc universally round up their prices to the nearest 10 or even 100 yen.
I do regret Japan rolling back their previous requirement to have all prices tax-included, since now many budget places do the US thing of advertising nice round numbers but adding the tax on top.
They increased consumption tax but made it conditional in some way I don't understand, so that taking items out of a convenience store was taxed more than eating inside it. So there wasn't a single tax inclusive price anymore.
Never had too many issues with coins in Japan (I did leave before the new coins though), and I had a tendency to try to spend my coins so never really accumulated enough that they were becoming a pain.
Luckily the conbini shops have machines that do take them and allow you to dump a whole handful of change in at once and will give change back in the minimal configuration. So my recommendation in Japan is when you buy something at the conbini, dump all of your loose change into the machine, then pay the rest with a ¥1,000 notes and you will get the minimal number of coins back.
Oh, and you can throw the ¥5 coins into the local shrine for good luck. :-D