Under Decree 58/2012, if an international treaty has provisions regarding foreign ownership limit (FOL) in a public joint stock company then the provisions of the international treaty will apply. Under Decree 118/2015, if a foreign investor is subject to multiple international treaties on the same industry or business line then the foreign investor is entitled to select one of the applicable international treaty. And if the foreign investor has selected to follow one international treaty then the investor will need to comply the provisions of such international treaty as a whole.

A Japanese investor is entitled to the following international treaties between Vietnam and Japan concerning foreign investment in Vietnam:

The Commitments of Vietnam to the World Trade Organisation (WTO Commitments);
The Bilateral Investment Treaty between Vietnam and Japan (VJ BIT);
The Agreement For An Economic Partnership between Vietnam and Japan (VJ Partnership); and
The Agreement On Comprehensive Economic Partnership Among Japan And Member States Of The Association Of Southeast Asian Nations dated 2008 (ASEAN-Japan Partnership).

Under Decree 118/2015, when investing in Vietnam, a Japanese investor will need to select one international treaty among those listed above. Among these treaties, the VJ Partnership seems to give a Japanese investor the most advantages. This is because Article 9 of the VJ Partnership provides that:

Vietnam and Japan reaffirm their rights and obligations under the WTO Agreement or any other agreements (which should include the ASEAN-Japan Partnership) to which both Parties are parties; and
the VJ Partnership is incorporated into and form part of the VJ Partnership.

As such by selecting the VJ Partnership, a Japanese investor would effectively preserve all of its rights under the WTO Commitments, VJ BIT and ASEAN-Japan Partnership. According to the guidance on how to apply various international treaties to determine conditions for foreign investors published by the Ministry of Planning and Investment (“MPI”),

A Japanese investor would be treated in the same manner as a Vietnamese investor except for the sectors listed in Annex I and II of the VJ BIT (see here). This is provided in Articles 2 - 5 of the VJ BIT;
For sectors listed in Annex I and II of the VJ BIT, a Japanese investor should be permitted to invest to the extent that such sectors are permitted in any of WTO Commitments, VJ Partnership and ASEAN-Japan Partnership; and
For a sector listed in Annex I and II of the VJ BIT but not provided in any of WTO Commitments, VJ Partnership and ASEAN-Japan Partnership or not committed by Vietnam in these treaties, a Japanese investor should be permitted to invest to the extent that such sectors are permitted by Vietnamese law.

Vietnam Business Law