This is the opposite of my experience.

Can you describe why you thought the food in Japan was expensive and what you were typically paying for meals?

For me:
800yen to 1,000yen will get you a very generous lunch (often several courses) at an upmarket restaurant (Osaka is an amazing city for this!)
You can even get elaborate kaiseki style menus or meals from Michelin starred restaurants from around 2,500yen if you stick to lunch times (the same restaurant may offer a similar menu for over 5 times the lunch price in the evening)

and for evening meals I typically spend between 600yen and 800yen when travelling on a budget.
Sometimes from more downmarket restaurants or noodle joints, occasionally by getting discounted bento at department store typically on offer around an hour before closing time (up to 80% off with a 50% discount being quite typical). At the same time I might pick up discount breads and pastries for breakfast. Next morning I pop them into a paper bag and blast the contents for 1 or 2 minutes with a hairdryer for just-baked freshness.

If you're not worried about salt and fat intake there are lots and lots of very tasty economic options available at any time of the day for under 300yen in any Japanese city.