We can be pretty sure it isn't in Japan. The two most referenced sites are:
However, both stake their claims by virtue of their proximity to Golgotha. (Proponents of the two tomb sites also disagree on the location of Jesus' crucifixion.) However, I don't see anything in the Gospel texts that indicate where the tomb might have been in relation to the crucifixion site:
And when evening had come, since it was the day of Preparation, that is, the day before the Sabbath, Joseph of Arimathea, a respected member of the council, who was also himself looking for the kingdom of God, took courage and went to Pilate and asked for the body of Jesus. Pilate was surprised to hear that he should have already died. And summoning the centurion, he asked him whether he was already dead. And when he learned from the centurion that he was dead, he granted the corpse to Joseph. And Joseph bought a linen shroud, and taking him down, wrapped him in the linen shroud and laid him in a tomb that had been cut out of the rock. And he rolled a stone against the entrance of the tomb. Mary Magdalene and Mary the mother of Joses saw where he was laid.—Mark 15:42-47 (ESV)
We know who the tomb belonged to, but not where it was situated. In fact, I can see no reason for the tomb not to be anyone of Second Temple burial sites found around Jerusalem. Given the little we know about Joseph, I'd say the Sanhedrin Tombs1 are as likely than any other candidate. More likely still, the tomb was used by Joseph's family and the connection to Jesus was lost.2 It may very well have been destroyed in one of Jerusalem's many rebuilding projects.
Can we know where Jesus was buried?
1. Oddly, it's difficult to find good information on this site, which is practically neglected. I don't know, for instance, exactly how they got their name or what era they come from. So this suggestion ought to be taken with a shaker of salt.
2. This theory isn't surprising since according to the Gospels, the tomb would have been empty. There was nothing to see and no reason to visit!