According to this New York Times article, one reason is that the Japanese value ethnic homogenity. 98.5% of the country's population is ethnically Japanese. This may be contrasted with countries like the United States, which are significantly more ethnically diverse. Other relatively developed countries, like Israel, Hungary, and Poland offer similar nationalist justifications for their decision to not take in a significant number of refugees. Commentators have also noted that Japan has had no issues with Islamic terrorism, unlike countries who have a more welcoming attitude towards immigrants and refugees from majority-Muslim countries.
As for your question regarding criticism from NGOs and newspapers, that's slightly unclear. Anecdotally, as a consumer of mainstream media outlets, I've noticed that American media outlets naturally focus first on the American politics, then on European politics (given the broad cultural similarity between Europe and US) and then on politics elsewhere in the world. This would explain why the issue of Japan and refugees tends not to be raised very often.
If you mean to ask why the issue isn't raised in Japanese media and, more broadly, Japanese society, then that's a better question. Again, it likely has to do with the prevailing political and cultural norm that ethnic homogenity is desirable. That said, the issue is nevertheless often discussed in Japan as well.
One must also keep in mind that following the events of the Second World War, ethnic nationalism is something that much of Western Europe, and particularly Germany, has broadly repudiated in some sense. Until very recently, nationalist parties were considered entirely outside of the mainstream of European politics, and, to my knowledge, no nationalist party has had power in a Western European country for quite a long time. Wikipedia, for example, describes German nationalism as being "taboo" in Germany (a scholarly source is given for this claim). Even in the United States, given its history of racism and slavery, ethnic nationalism isn't something within the mainstream of political discourse; this is why events like the Charlottesville rally are repudiated across the political spectrum. This may again be contrasted with countries like Japan, Israel and India, all of which, although having relatively Western political systems, have nationalist political parties in power, all of which would likely be considered "far-right" by European/American standards.