Nagasaki is correct. It’s worth noting the biggest reason for this, in the context of what somebody upthread said about Christianity being criminalized in the 16th century. The interesting thing about the “Christian persecution” in Japan at that time was that it wasn’t exactly a “religious” persecution. That is, the objection to Christianity was not based on the fact that it conflicted with Shinto or Buddhism. Rather, it was political in nature.
In the 1600s, Japan was going through a period of “disunity”. That is, the Emperor was pretty powerless and the country was divided up into a number of small districts that were unified only in the most technical sense. These various districts were frequently in conflict with each other as their respective daimyos (feudal lords) vied for supremacy. Enter the (mostly Portugese and Dutch) Christian missionaries. These missionaries arrived on the same ships as European merchants/traders, who began to introduce all sorts of new products into Japan.
The most significant new product was, unsurprisingly, firearms. The Japanese had up until then still fought medieval-style, with swords and spears and archers, etc., and they eagerly adopted the new weapons the Europeans introduced.
Eventually, though, it occurred to various daimyos around the country that rival daimyos who happened to control major ports (like, say, Nagasaki) could end up with a dramatic military advantage, due to the simple fact that the guns entered the country at those locations. It would be a relatively simple matter for those daimyos to either purchase all the guns for themselves as soon as they entered the country, or simply prevent the traders from traveling to other districts. Pretty soon, these port-controlling daimyos would severely outgun everybody else.
The solution? Throw 'em all out. While it was specifically the merchants who were bringing the guns into the country, the fact that the missionaries arrived with the merchants led to the not-unreasonable conclusion that they were one and the same. So they were barred from the country, and the religion was criminalized . On one hand, there was likely suspicion that converts might be used by the Europeans to smuggle guns into the country, and on the other, by pointing to the religion (and it’s incompatibility with traditional beliefs) and not the merchandise, they deflected attention away from the fact they were depriving the people of all the goods the merchants brought.
The daimyo of the district that included Nagasaki was more tolerant (he’d gotten rich from the trade, after all), and many Japanese Christian converts fled to Nagasaki to escape persecution in the other regions, and the religion continued to flourish there.
The Wikipedia article on Nagasaki has some good information, though much of what I’ve shared here came from an English-language Japanese news Web site (it was actually more Japanese-written essays than actual “news” - I read a really good essay written by Japan’s current Emperor there), which I read several years ago and unfortunately no longer have a link to.