Where in Japan do you intend to travel? In what season? Just outside major cities are rural and farming areas. In fact, some parts of Tokyo, one of the biggest cities on earth, are under cultivation.
Just outside Tokyo, Chiba Prefecture has many rural landscapes and farm experiences. Chiba City has large areas under cultivation where you find Yokota Farm. On the farm, you can harvest food and cook it. The surrounding area is vibrant green in spring and summer.
If you're up for cycling, you can bike from central Chiba City across the wards going east towards the ocean. The ride takes about 2-4 hours past farms, fields and forests.
For families, Mother Bokujo (Mother Farm) is recommended. Sheep shows, cow milking, fruit picking and amusements keep everybody happy. The fruit picking is nearly all year long. Many people are surprised that strawberry picking starts in December. Check the
If you'll be visiting Kyoto, consider staying at Miyama, a village of thatched houses. You can fish, pick fruit, and learn crafts here. The village feels very remote from everything, and the night skies are full of stars. You might have heard of satoyama landscapes - places of cultivation on the edges of forests. Miyama has this kind of cultivated and wild landscape.
I live in Niigata right now, and if you're after agriculture I think it's a top spot to visit. The area is known for rice planting, specifically the highly regarded koshihikari rice. It's also an incredibly picturesque part of Japan - beautiful mountains, fresh flowing snow melt water rivers, and it's different in every season.
It's also very accessible from Tokyo - you can reach Niigata City within about 2 hours from Tokyo. My area of Niigata Prefecture is about an hour and a half from Tokyo on the Joetsu Shinkansen.