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The Ministry of Health Welfare and Labor has issued an update that is directed at Companies.
This time we will address the Non-Work Allowance.
That said, companies are really being asked to respond over and beyond the guidelines.

Given the current situation and depending on individual Companies and should the work being performed be conducive to working from home, that really is the best situation. If you have any questions about the requirements and operations of working from home please feel free to consult with us and we would be happy to assist.

The full details of the guidelines from the Ministry below:
https://www.mhlw.go.jp/stf/seisakunitsuite/bunya/kenkou_iryou/dengue_fever_qa_00007.html (Japanese only)

In summary!
When a worker has a fever or cold like symptoms.
If you have a worker with a temperature or cold like symptoms please ask them to take leave. Taking leave is important for yourself, but it is also an important step in preventing further infection. In order to prevent further infection companies and society need to understand. Creating an environment whereby workers can take leave requires cooperation Is the message.

When an infected worker is on leave:
In the case of COVID-19 infection, the Prefectural Government can require that the workers take leave and as the illness cannot be attributed to the Employer there is no need to pay the Non Work Allowance . (PMP: The Prefectural government needs to confirm this)
When an employee is unpaid leave due to an illness, and in the event certain requirements are met, after three days of being absent from work, without pay, the employee should be entitled to receive an allowance through the health insurance association of up to two thirds of the average of their monthly salary over a 12 month period for the duration of their absence. The employee needs to apply for this allowance through the Company, who also need to confirm information in the documents that need to be submitted to the Health Insurance Association.

When a worker could be infected and is placed on Leave:
If a worker who based on the results of the COVID-19 Consultation center can continue their duties, but the Company at their discretion determines the worker should be on leave, then in this situation the reason can be attributed to the Company and the Non Work Allowance should be paid.

When a worker has a fever:
When COVID-19 has not been diagnosed, but the worker has a fever or other symptoms and the Company recommends, on the advice of the government, that a worker should be on leave, then this leave should be treated as standard sick leave.

How to use Sick Leave:
In the situation when the Company determines that all workers who have a fever of 37.5 or above need to take leave, this would see the illness as being attributable to the Company and hence the Non Work Allowance needs to be paid.
Additional Comments for English Readers, that were not in the Japanese version.
Should your Company have paid Sick Leave, then employees can certainly choose to utilize this leave. With this leave the Company can also suggest the employee to utilize this leave.
Employees can also choose to use their annual paid leave, but Companies cannot require Employees to use their annual leave.
If the Employee has no remaining Sick Leave and does not want to use their Annual Leave then the Non-Work Allowance comes into play. Employees cannot be penalized for utilizing this Allowance.