Yes. A party can seek an order of the court for production of documentary evidence held by the other party or third party. It is called Document Production Order ("Bunsho Teishutsu Meirei"). However, it is required to specify the document, which is not disclosed, to be prepared for the other party. And it is not often used.

Japanese system does not allow a deposition outside the courtroom.

Parties can request the judge to summon witnesses from the opposing or third party, in addition to offering its own witnesses, for cross examination in the court.