the "nurses" from the philippines and indonesia, for that matter too, are in most cases here through the bilateral FTA (or EPA as the are called here) giving them the opportunity to stay and "work" in japan for the purpose of obtaining a qualification as a nurse (看護士) or as a certified careworker (介護福祉士). in addition these workers have to appointed be the government of the philippines or indonesia. now, if they fail to pass the exam(s), they will need to leave japan.
for more on this
http://www.mofa.go.jp/region/asia-pa...609/annex8.pdf
from JP forum's self-proclaimed pseudo-expert on japanese trade policy