Whilst sexual orientation is not directly protected under Japanese law, it is nevertheless important not to discriminate against someone simply because of their sexual orientation.

Sexual orientation can be defined as:

• Orientation towards persons of the same sex (homosexual)
• Orientation towards persons of the other sex (heterosexual)
• Orientation towards persons of the same and the other sex (bisexual)

Note: The term ‘Homosexual,’ is now no longer considered acceptable in many countries. Thus ‘Lesbian’ and ‘Gay’ are preferable.

This principal of antidiscrimination should apply to all forms of employment, training, recruitment, promotions, transfers, and dismissals.

You should not:

• Discriminate indirectly against anyone – that is, to apply a criterion, provision or practice which disadvantages people of a particular sexual orientation unless it can be objectively justified
• Subject someone to harassment. Harassment is unwanted conduct that violates a person’s dignity or creates an intimidating, hostile, degrading, humiliating or offensive environment for them.
• Victimize someone because they have made or intend to make a complaint or allegation or have given or intend to give evidence in relation to a complaint of discrimination on grounds of sexual orientation
• Discriminate against someone, in certain circumstances, after the working relationship has ended.

Here is an article on LGBT rights in Japan.