Elizabeth Aruoriwo Obueza was detained two weeks ago after authorities turned down an appeal against her asylum rejection, Obueza and her lawyer told Reuters.
Obueza, 48, campaigns for asylum seekers and the 4,700 people on "provisional release" from immigration detention - a status that lets foreigners out from detention but bars them from working and travelling freely.
Obueza's arrest is part of a wider campaign by the Justice Ministry, which in September 2015 said it would take steps to reduce the 60,000 foreigners living in Japan without visas. People on provisional release, many of whom have lived in Japan for decades, have been among those targeted, activists and lawyers say.
"Elizabeth was targeted and detained for being an activist," said immigration lawyer Shoichi Ibusuki.
"I want her released immediately."
The crackdown on people like Obueza comes even as people on provisional release, despite being legally unable to work, power Japan's construction and manufacturing sectors as companies scramble to find workers in the worst labour shortage in decades.