The Government has been promoting teleworking as part of Work Style Reforms since 2018. I don’t think it went well. However, the new coronavirus outbreak seems to be achieving the same goal in just a few weeks. I will briefly explain the laws relevant to introducing working from home to companies.
How to change working conditions
As a workplace is one of working conditions agreed between parties, if an employer wants to have their employees work from home instead of an original workplace, employees’ consent is required. 
However, where rules of employment are prepared, the employer may change the working conditions by amending the rules provided (a) the change is reasonable and (b) the employer let them know the change of the rules. 
Rules of working from home
Rules of employment is required to be prepared in a company that employs 10 or more workers. 
Employers may insert provisions related to work-from-home policies into existing rules of employment or may create rules of working from home as a separate set of rules.
1. Labor Contracts Act
Article 8: A Worker and an Employer may, by agreement, change any working conditions that constitute the contents of a labor contract.
2. Article 9: An Employer may not change any of the working conditions that constitute the contents of a labor contract in a manner disadvantageous to a Worker by changing the rules of employment, unless an agreement to do so has been reached with the Worker; provided, however, that this does not apply to the cases set forth in the following Article.
3. Labor Standards Act
Article 89: Employers who continuously employ 10 or more Workers shall draw up rules of employment covering the following items and shall submit those rules of employment to the relevant government agency. In the event that the Employer alters the following items, the same shall apply: (Omitted)
Of course, a company that does not employ 10 or more workers may also have rules of employment and rules of working from home. Even if it wants to avoid any hassle, it would be worthwhile considering such rules, regardless of its formality.
Provisions to be inserted
Among other provisions, it will be advisable to set out provisions regarding, at least, (a) ordering working from home, (b) working hours for remote workers, and (c) who bears communication expenses such as high-speed internet.
The sample rules of working from home (Japanese) prepared by the MHLW is available.
Hanko as an obstacle
It has been reported that many workers are being forced to commute to their offices because of a reliance on hard-copy paperwork for contracts, and the need to be stamped with seals despite the pandemic. However, hanko or seals are not a legal requirement on concluding a contract. Please read my previous articles: Exchanging contracts in Japan: seals and signatures (1) and (2).
Disclaimer: While every effort has been made to ensure that the information on this article is accurate at the time of posting, it is not intended to provide legal advice as individual situations will differ. If you do require advice or wish to find out more about the information provided and related topics, please contact the author.