Well, in all likelihood it's a reaction to having discovered that a wanted terrorist was living a quiet life in Japan for more than six months and left again before anyone realised he was even here! It was most embarrassing for the government and this is probably the only thing they could think of as a countermeasure. In all likelihood it won't be that effective either, but politicians will respond that "at least we are doing something".

As to those US citizens who take umbrage at Brazil and Japan adopting similar measures to the US. I wouldn't look on it as being retaliatory (after all, the Japanese are NOT singling out US citizens as the Brazilians are), but consider that imitation is the highest form of flattery