where in tokyo?

there is the youth hostel in yoyogi koen. also temp housing all over but that can be expensive. a proper apt is not so attractive for short-term stays because it needs payment of key money (a gift of 2 months rent usually, not refundable).

weekly mansions are probably the easiest to arrange from afar.

you should consider writing to the office you will intern at and ask if they have a recommendation.

i don't know actually if its cheaper. i just know that some visiting studios made use of it for extended stays for the students. i don't know the logistics of it all, but assume it was the cheapest (if not most comfortable) option. good part of town though and pretty close to bunkyo-ku.

bunkyo-ku is host to my alma-mater. am pretty sure there is low-cost housing in the area to accommodate all the students. it is also nice part of town in my opinion. you can still see remnants of the past in the streets and buildings, plus there is ueno park right there, with the corbu museum right next to the fantastic theatre by kunio maekawa, a very nice library by ando, and the horyu-ji treasure museum by taniguchi. AND a zoo. who could ask for more?

in general if the internship is not very long i would recommend finding a place that doesn't expect key money. that kind of rules out anything in the normal rental market, unfortunately... hopefully your office will have some good advice.