The automaker says "market dynamics" prevent it from competing effectively in both of the countries, so it will cease operations and concentrate resources elsewhere.
The company says in an emailed statement that the decision was communicated to employees and dealers on Monday.
Ford says that it will contact customers to explain its commitment to servicing cars, providing parts and making warranty repairs.
The markets are not big ones for Ford. Last year it sold only 6,100 cars and trucks in Indonesia and only 5,000 in Japan.
In Japan, the market is dominated by domestic brands including Toyota and Honda.
Also on HuffPost