The Japanese government explained at the House of
Representatives on May 29 that the foreign companies (with branch in
Japan) are not eligible for the subsidy program (Jizokuka Kyufukin 持続化給付金).
You can see the actual discussion in the video linked here.
See around 4:29:50 of this video.
For now, it is not possible for foreign companies to apply for the subsidy program.
We’ll provide information here, if we catch any update about this matter.
Acceptance of Requests for Subsidy Program for Sustaining Businesses Starts
Ministry of Economy, Trade and Industry (METI) website