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Effective as of April 7th, Tokyo, Kanagawa, Saitama, Chiba, Osaka, Hyogo and Fukuoka will be under "emergency state". What does this mean? 

First of all, Tokyo and other prefectures won't be shutting down like in other countries, because Japan does not have that in the constitution. 

（As of April 6th 2020）

▼Those that deffinately will be asked to shutdown 

Educational facilities such as universities, cram schools, and driving schools
Exercise facilities and playgrounds such as gymnasiums, swimming, bowling, skating, golf, batting, and sports clubs
Theaters such as cinemas, live houses, and theaters
Facilities related to gatherings and exhibitions such as public halls, museums, museums, and libraries
Recreation facilities such as cabarets and nightclubs, dance halls, bars, private room video stores, online cafes, manga cafes, karaoke stores, mahjong stores, pachinko stores, game centers, etc.

Regarding department stores or shopping malls, home centers will be partially open since they have medicines and food. Check individual web sites to see if they are open. 

*If the stores are as small as 100 square meters, it may open with strict 
Infection prevention measures.

▼Facilities that need to be open as a lifeline

Medical facilities such as hospitals or pharmacies 
Supermarkets or convenience stores, other whole sale stores with food 
Hotels and other accommodations
Trains, bus, taxies, rental cars, ships and airplanes and other methods of public transportation/deliveries 
Factories 
Financial institutions and public services 
Public bath 
*Restaurants may open with strict 
Infection prevention measures.

*Izakaya and bars may be asked to be closed. 

▼Limitation to go out

According to the regulation, the Metropolitan government can ask you to "stay home" but this does　not　mean　that　you　are　banned　from　going　out　to　go　to　a clinic　or　to　get　some　food　or　daily　necessities. 

▼Schools 

Under the regulation, all public and private schools will be closed. However, there is no sanction for opening. 

▼Facilities and stores 

The prefectural governor will also be able to “request” the use of facilities if necessary to prevent the spread of the infection.

Under Act on Special Measures Article 45, term 2 "facilities that are used by many" are the target of "request for closure".

This includes ▽ movie theaters and theaters, convention halls and exhibition halls, ▽ department stores, supermarkets, ▽ hotels and inns, ▽ gymnasiums, swimming pools, and other sports facilities ▽ museums and libraries, ▽ nightclubs, ▽ driving schools, Facilities that have a floor area of ​​more than 1000 square meters, such as cram schools or driving schools, and facilities that are less than this requirement will be eligible for the criteria if  necessary.

▼Events 
Under Act on Special Measures Article 45, term２, Mayor can ask to stop events even though it does not hold the power to sanction those who do not obey.

▼Lifeline 

Lifeline including electricity, gas, water won't stop. Also, shipping, telephone, internet and postal office will not stop. Public transportation won't stop. 

▼Masks
Under the Act on Special Measures Article 55, the Japanese government can ask wholesale to sale necessity items such as masks. Aside from Act on Special Measures, the Japanese government has bought off masks and already has sent to the Hokkaido area and medical facilities under Act on Emergency Measures for Stabilizing Living Conditions of the Public. (http://www.japaneselawtranslation.go.jp/law/detail_main?re=01&vm=04&id=2802)

▼What the Japanese government can force you to do:  

When a state of emergency is declared, what the government can do is: to use land and buildings without the consent of the owner, if necessary to create a temporary medical facility; and to ask the storage necessary supplies such as medicines and food.

Hiding or discarding supplies without following the order will result in imprisonment for up to 6 months or a fine of up to ¥ 300,000. If you refuse to inspect the storage area, you will be fined 300,000 yen or less. Only these two have legal power and penalties.

▼Medical institutions, nursing homes, daycare, hellowork (Public Employment Security Office）

Hospitals and pharmacies, local clinics will remain open. 

However, each municipality has decided to make adjustments, such as setting up medical institutions that will focus on infected patients in preparation for the peak of infection, and moving patients with other diseases to another medical institution. *Some pharmacies may make some adjustments as well.  

In addition, the Ministry of Health, Labor and Welfare has a policy to increase the availability of “online medical treatment” through the Internet. It has been considering changing the current rules to require face-to-face medical treatment by doctors for the first consultation and rather make online consultation available even for the first time. 

＊See the list of clinics that are open for online medical treatment 

https://doctorsfile.jp/search/ft104/

▼Nursing homes

The prefectural governor of the region where the emergency was declared can request restrictions on use or suspension of work only for day-service facilities and short-term stays. On the other hand, nursing homes or group homes, home-visit care may remain open with strict infection prevention measures. 

▼Daycare

The government and municipalities can ask daycare to be closed. However, municipalities may provide alternative childcare services for healthcare professionals, those who must work to maintain social functions, and those who need to take care of children, such as single-parent families who cannot take time off work.

▼Public Employment Security Office
The Public employment security office will continue to open. However, they may limit their operation hours depends on the infection rate of the community. If in any doubt, contact them via phone first. 

（As of April 7th 2020）

▼Public transportation 

All public transportation such as subway, trains, buses and bullet trains will operate. However, each company will consider reducing or suspending service as necessary depending on the future situation, such as receiving special requests from the government or local governments, and further fall of users. Check the latest information on the homepages.

▼Airline 
Airline operations will be limited. Please check the website for updated information. 

▼Taxi
The following companies will remain open with strict preventative measures. However, they may reduce operation hours and drivers. 

Kokusai motorcars 
Daiwa Motor Transportation Co., Ltd.
Teito Tacxi
HINOMARU KOTSU Co., Ltd.

▼Supermarkets and Convenience sores 

All supermarkets and convenience stores (such as seven-eleven, family mart and Lawson) will remain open though they might close earlier than regular hours. 

▼Drug stores
All (except for some individually ran small drug stores) will be open with limited open hours. Check their website for operating hours. 

▼ Department stores 

Under the deceleration of state of emergency, some will close. 

Mitsukoshi Isetan has closed 6 shops including Nihonbashi, Ginza, Ebisu, Shinjuku, Tachikawa and Urawa. Online shopping will be still available for necessary goods such as food. 

Matsuya will be closed for both Ginza and Asakusa stores. 
Odakyu will be closed for Shinjuku and Machida sores except for food floor but they also will be closed for weekends. 
Atre of JR east Japan will close shops except for food floor. 
Lumine of Ikebukuro, Yurakucho, Shinjuku, Lumine est Shinjuku, NEWoMan Shinjuku will be closed. 
Other department stores may remain open for food and other daily necessities. 

▼Restaurants and generally eating out

- Family restaurants 

All family restaurants may open and skylark holdings may increase its delivery and takeout.

- Fast food 
McDonald's has stopped operating for 24 hours. 440 stores out of 1130 will limit opening hours for two hours and open until 8 pm. (effective as of March until 6th of May) 

- Coffee chains
Starbucks will be open under limited hours of operation (around 7 pm). 
Tullys' will limit their operation down to 250 shops out of 750 around the country. 

Beef bowl (gyudon) chains may remain open under limited hours and staffs. 

▼ Financial institutions 

All banks' ATM internet banking, transactions through the application will remain open. However, some ATMs in shopping mall may be closed as they will operate under limited hours or will be closed. 

Nevertheless, under the declaration of the state of emergency, a small branch may be closed temporarily. 

Consultation desk for government financial institutions
Japan Finance Corporation (JFC) and Shoko Chukin Bank, which are the points of contact for government funding support measures, such as receiving loans substantially free of interest and support for cash flow will continue to function.

▼Banks of Japan

All banks will be open. 

Stock exchanges, etc.
The Japan Exchange Group will also be able to trade stocks and futures products as usual on the Tokyo Stock Exchange (TSE), the Osaka Exchange, and the Tokyo Commodity Exchange. 

▼Telecommunications

Under the government's demand, NTT docomo, NTT higashi nihon, NTT nishi nison, au KDDI , softbank will continue to provide services. 

▼Postal service/delivery services

Japan post, Yamato, Sagawa will remain open. However, some offices are considering canceling direct operations, and there are chances where the collection and delivery of luggage may be delayed, and we are calling for updates on our website and other sources.

▼Life line

Electricity & Gas 

Even after the employee's commute was to be restricted, gas and electricity will be providing services.