There are some local hospitals and clinics that are on duty under the rotation (Rota) system at night and on weekends. Check the website of your local medical association. For example, if you live in Bunkyo-ku find Bunkyou-ku Ishikai page (Bunkyou-ku Medical Association) and search for the clinics/hospitals on duty. Many places are open until around 22:00. On weekends they may close earlier. Make sure you call the clinic/hospital you wish to visit before you go to see if they accept patients.

Information about clinics/hospitals on duty is also available by telephone services. In Tokyo call Himawari and multilingual staff will find a clinic/hospital on duty for you. Himawari is open from 9am to 8pm everyday.

It is very important to call the clinic/hospital to see if they can accept you before you visit on weekends or at night. Due to the limited number of staff at night or weekends, it is not guaranteed that the clinic/hospital can treat a patient at the particular time you want to visit. In that case you will need to find another place to go. In particular, after midnight, public holidays, New Year and the Bon holidays there are a only few institutions available, so If you have a symptom before long holidays it is strongly recommended to see a doctor as early as you can.
Also, if a clinic/hospital you have been to as a patient before accepts after hour patients, call and ask if they can treat you. Because you are a returning patient they have your information on file, so you have more chance to be accepted.

Because the number of clinics/hospitals with foreign language speaking staff is very limited on weekends or at night, if you don't speak Japanese ask someone who can speak Japanese to call and possibly go to the clinic/hospital with you.

Bring your health insurance card and ID. Making payment at after hour or on holidays can be different to weekdays, so it is safer to bring more money than usual. Big hospitals usually have an ATM located in the building.

Important points

If possible, call and visit a clinic/hospital you have visited before.

Ask someone who can speak Japanese to call and see if they accept patients. If you can speak Japanese emphasize to the hospital staff that you can speak Japanese.

If you don't speak Japanese, ask someone who can speak Japanese to go with you if possible.

Don't forget to bring your health insurance card. Also, please take enough money, as it may be difficult to guess how much it will cost.

When your symptom or injury is serious and you cannot judge if you should call an ambulance, there is a telephone consultation service available from the Tokyo Fire Department. Ask them if your symptom/injury requires ambulance. English speaking staff is available if you call within 23 wards of Tokyo.

Tokyo Fire Department Telephone Service

Within 23 wards of Tokyo： 03-3212-2323
Tama area： 042-521-2323
Or press ＃7119 on your telephone

Tokyo

Web Page of Tokyo Joho

http://www.japan-city.com/tokyo/htmb/benri111 (Japanese only, please try http://translate.google.co.jp/ for translation.)
It has links to the pages of local medical associations.

Web Pages of Tokyo Fire Department

http://www.tfd.metro.tokyo.jp/kb/index.htm (Japanese only, please try http://translate.google.co.jp/ for translation.)
You can find the information on emergency hospitals on that day.

Tokyo Metropolitan Health and Medical Information Center (Himawari)

TEL： 03-5285-8181　Open everyday 9:00～20:00
http://hokencenterkomaba.c.u-tokyo.ac.jp/indexk.htm
English Pages available.
Himawari provides information about medical institutions with staff who speak several languages and provide information about medical and health insurance systems in Japan.
English, Spanish, Chinese, Thai and Korean speaking staff available. They will try to find a medical institution according to your needs (for example, if you are looking for a clinic near your station, a clinic open on holidays or to find a female doctor).
Himawari is also available with a Japanese operator 24 hours a day (automated service after 20:00).
Please note Himawari can offer interpretation services if a medical institution calls on behalf of you.

Chiba

Chiba Medical Association page has search engine for finding a clinic/hospital

http://www.chiba.med.or.jp/
English, Chinese and Korean pages available, located below the top page.

Chiba emergency medical information

http://www.qq.pref.chiba.jp/ (only Japanese please try http://translate.google.co.jp/ for translation.)

Saitama

Saitama Medical Association page has search engine for finding a clinic/hospital

http://www.saitama.med.or.jp
Only in Japanese. Click 「病院検索」 button. Please try http://translate.google.co.jp/ for translation.

Saitama Emergency Medical Information Center

http://www.saitama.med.or.jp/center/emergence_guide.html
TEL： 048-824−4199
Telephone service to find clinics/hospitals 24hours.

Kanagawa

Search Clinics/Hospitals in Kanagawa

http://www.kanagawa.med.or.jp/ (Only in Japanese please try http://translate.google.co.jp/ for translation.)

Kanagawa Emergency Medical Information System

http://www.qq.pref.kanagawa.jp/qq/qq14tpmnlt.asp (Japanese only please try http://translate.google.co.jp/ for translation.)

Telephone services (24h/365days)

Yokohama Emergency Medical Information center
TEL： 045-201-1199

Kawasaki Emergency Medical Information Center
TEL： 044-222-1919

Kamakura Emergency Medical control center
TEL： 0467-24-0099

Sagamihara Emergency Medical Information Center
TEL： 0427-56-9000

Ibaraki

Emergency Medical Information System

http://www.qq.pref.ibaraki.jp/
TEL： 029-241-4199
Japanese and English pages available.
24h telephone service to find clinics/hospitals.