The first three candidates will begin training next year, and if the experience is successful the job will be opened up to women, explained Jean-Yves Le Drian on Tuesday.
Until now, women in the French Navy have been barred from submarine duty, which involves two and a half months without interruption under water, twice a year.
Among the physical risks of submarine life is an elevated level of carbon dioxide, which is apparently more likely to harm women than men.
Few people of either sex are suited to a lifestyle which involves long periods away from loved ones back on land and little privacy aboard.
In February a book on sexual harassment in the French army created considerable concern.
No such book about the French navy has been written but the importance of good professional relationships between the sexes in the confined space of a submarine is paramount.
At the moment, only nuclear weapons-carrying submarines are large enough to accommodate women but all French submarines built or renovated from 2018 will be equipped with facilities for women.
Since 1993 France’s naval school has trained around ten female officers per year and of those, only 23 have commanded or are now commanding vessels.
Many women as well as men turn down operational jobs for the sake of their family lives at around the ages of 30-35, when they might be ready to take command.