In short, mostly yes if they have the Mastercard logo. Just make sure you have cash to hand as well, and getting an IC card like a Suica card or Pasmo card is handy too, as they work as prepaid cards and work in more shops as well as vending machines.
In long, over the past few years, I’ve found more shops accepting Mastercard and Visa around places frequented by foreign tourists, but there’s still plenty of places that are cash only, especially as you get away from the crowds. I do try to keep a Suica card topped up for use with vending machines and some shops that take IC card and cash but not Mastercard, to try and minimise my cash use, but there’s plenty of places that are still cash only. Do also note that Japan has lots of other payment methods, such as QR-based ones, like PayPay, or JCB, the Japan Credit Bureau credit cards that use their own network separate to Visa and Mastercard. I’d just recommend keeping cash to hand as a backup and then get some more out if you end up using it.