Hi Alma san,
Yes, there's one in Setagaya-ku.
It's run by Setagaya-ku, information in Japanese here.
http://www.city.setagaya.tokyo.jp/030/d00004059.html
(Could not find it in English section, though.)
Here's an old article on swimming pools in Osaka and Tokyo (from The Japan Times July 2001 issue - maybe this is the one you've found?)
http://search.japantimes.co.jp/cgi-bin/fl20010701a7.html
---- quote ----
Setagaya Kuritsu Sogo Undo-jo: Indoor 50-, 25-meter and children's pools, at 4-6-1 Okura, Setagaya-ku, reached by bus from Futako Tamagawa Station, Tokyu Denentoshi Line, or Seijyo Gakuen Station, Odakyu Line. Closed 3rd Mon. (2nd Mon. in July, open daily in Aug.; 400 yen for adults (2 hours June-Sept., whole day Oct. to May). Call (03) 3417-0017.
---- unquote ----
It seems that the swimming pool was newly built since then, in new premises.
Now it's located at:
Funabashi 7-9-1, Setagaya-ku, Tokyo
Tel: 03-3789-3911
(Its office is still at Okura.)
Access:
1. "Daito-gakuen" stop by the bus running between Chitose-Funabashi and Kibougaoka Danchi.
2. "Asahi Shinbun Sha mae" by the bus running between Chitose-Funabashi and Umegaoka station or
Hachiman-yama Station and Kibougaoka Danchi.
3. "Houshouji" by the bus running between Umegaoka Station - Chitose Fuanbashi
4. "Chitosedai 6 chome" by the bus between Chitose-Karasuyama Sta. and Chitose-Funabashi Sta.
Open:
9:00 ~ 21:00
Closed:
1st Monday of the month, End of the year (usually around 28-30th Dec.) and New Years holidays (1st-3rd Jan) and maintenance day (no specific dates mentioned)
They don't close during August.
Admission:
Adult JPY400, Child JPY150
On Saturday, Sunday and public holidays during the months June - September the above fee is for 2 hours. Otherwise there's no time limit.
Oh, and the name of the swimming pool is Chitose Onsui Puuru (Pool).
It has a 25m course, you can swim while enjoying the nice view of green of the park next to the pool, according to the Setagaya-ku website.
It also has a training room, pool for children, a jacuzzi, an excercise room, etc. (Actually I cannot tell of they have only one room for each or several rooms of similar facility...
)
Parking lot is available (JPY100 for 30 min.)