Short answer. Yes, it can be. Article 815 authorizes a Filipino in a foreign country to make a will following the forms established by the law of that country, and such a will may later be probated in the Philippines. Following Japan's formalities while he is there is exactly what this article allows.
What the law says
When a Filipino is in a foreign country, he is authorized to make a will in any of the forms established by the law of the country in which he may be. Such will may be probated in the Philippines.
Civil Code, Article 815 — A Filipino Making a Will Abroad. Read the full provision →
The rule: foreign form, still valid at home
Article 815 addresses exactly your father's situation. When a Filipino is in a foreign country, he is authorized to make a will in any of the forms established by the law of the country in which he may be. A Filipino abroad is not confined to the formalities the Civil Code sets out for wills executed in the Philippines — he may instead follow whatever form Japanese law recognizes as valid for making a will there, since he is physically present in that country when he executes it.
Why Philippine law defers to the place of execution
This article reflects a practical accommodation for Filipinos living or working overseas: requiring strict compliance with Philippine formalities from someone physically in another country, dealing with foreign notaries, witnesses, and institutions, would make it needlessly difficult to execute a valid will at all. Allowing the will to follow local form removes that obstacle, so long as your father genuinely complies with what Japanese law requires for a will to be considered validly made there.
Probate still happens in the Philippines
Making the will under Japanese form does not strand it abroad. Such will may be probated in the Philippines. If your father's estate includes property here, or the will otherwise needs to be given legal effect in the Philippines, it can go through the Philippine probate process even though it was executed under a different country's formal requirements. The form of execution and the place where the will is later probated are two separate questions this article answers together.
What this does not decide
Article 815 addresses the *form* of the will — whether it was executed the right way. It does not by itself resolve every other question that could affect the will's validity, such as your father's mental capacity at the time or whether the will's substantive provisions comply with Philippine rules on heirs entitled to a legitime. Whoever eventually presents the will for probate will still need to show that it genuinely satisfies whatever formal requirements Japanese law actually imposes, since that is the standard this article points to.