Despite the popular political narrative in US, protectionism was very similar in both US and Japan. Japan was just more competitive in many areas. Japan did have gradually reduced number of import quotas like everyone else. 490 quotas in 1962 and 27 in eighties.
The most-favored-nation status came trough GATT agreement 1947 and it was not US favoring other countries. It was trade agreement. Japan joined 1955.
After 1979 Tokyo Round agreement, Japan had the lowest average tariff level among industrial countries, 2.5 percent against 4.2 percent for the US.
Before 1980, most of the friction in trade was generated by U.S. industries seeking protection from Japanese imports, including textiles, steel, televisions, and automobiles. Japan solved all these cases by agreeing to to voluntarily restrain exports of the disputed items.
Japanese markets were ridiculously hard to penetrate, but often the reason was not trade barriers. Usually it was just different customer preferences and sales channels. For example, at one time US companies offered cars to sale in Japan with left-hand side steering and complained about sales.
Japanese have very protectionist agriculture policies but this seems to be universal for everyone.