In the Fukanzazengi, Master Dogen did not have much to say about breathing during Zazen …

Let the tongue spread against the roof of the mouth. Let the lips and teeth come together. Let the breath pass imperceptibly through the nose. [NISHIJIMA]

But in his Eihei-koroku he wrote:

There is also the Mahayana way of regulating breathing. That is, knowing that a long breath is long and that a short one is short. The breath reaches the tanden [the area just below the navel] and leaves from there. Although the exhalation and inhalation are different, they both pass through the tanden. When you breathe abdominally, it is easy to become aware of the transciency [of life], and to harmonize the mind.

My late teacher Tendo said, “The inhaled breath reaches the tanden; however, it is not that this breath comes from somewhere. For that reason, it is neither short nor long. The exhaled breath leaves from the tanden; however, it is not possible to say where this breath goes. For that reason, it is neither long nor short.” My teacher explained it in that way, and if someone were to ask me how to harmonize one’s breathing, I would reply in this way: although it is not Mahayana, it is different from [the Lessor Practices]; though it is not [the Lessor Practices], it is different from Mahayana. And if questioned further regarding what it is ultimately, I would respond that inhaling or exhaling are neither long nor short. [Emphasis Added]