These figures seem rather contradictive. In the first, English totalise 3,9% (+3,5% from HK), and Germans 1,9% (no mention of other countries) of all foreigners in Japan. On
that page all Europeans account for just 2,5%. Worse, on the former American (US) take a a 13,5% share + Canadians 2,4%, but the total of North American falls to 3,4% in the 2nd page. guess the reason is that the first data is for non-resident (tourist, businesspeople, short-term visitors), while the second is for long-term resident only. Is that right ?
I had seen this site (in English) before but I couldn't find the number of EU residents and still can't.
I have found
this map which shows the clear difference in proportion between registered foreigners (residents) and others (visitors). Among residents, there are 4362 French people, 4163 Germans and 14438 British (don't know at what exact date they counted with such extreme accuracy

). Still don't know about Italians, Spanish and smaller countries...