Today there are mosques in every region of the country.
It's hard to say whether or not the actions of the Metropolitan Police and the National Police Association are indicative of Japan's attitudes towards Muslims.
For example, the Tokyo Metropolitan Government recently launched this guide book aimed at Muslim travelers: In November 2015, following the Paris attacks, a meme circulated on the English-language Internet about a list of supposed restrictions by Japan that effectively bans Muslim immigration. Muslims are allowed to visit, reside in and even become citizens in Japan.
Leading politicians including Prime Minister Abe Shinzo have also stressed the importance of tolerance.
In the 2014 court case related to the leak, the plaintiffs alleged: The Metropolitan Police Department and the National Police Agency had, as of 31 May, 2008, assessed and digitalized the personal information of ‘roughly 12,677 individuals’ equaling ‘roughly 89 percent of the 14,254 foreign nationals from Muslim countries registered in Tokyo,’ and later, by the time the Hokkaido Toya Lake summit convened in July of that year, had ‘profiled roughly 72,000 individuals from OIC (Organisation of the Islamic Conference) countries (assessment rate of 98 percent).’ Earlier in 2016 the group asked the Supreme Court of Japan to rule on the legality of the surveillance.The documents included the names, addresses and other personal information of Muslims residing in Japan.