Although the recent earthquake and the ensuing flood are horrific in scale, there is no prophecy in the Bible specific to Japan that I am aware
Earthquakes in various places (like wars, famines and disease) are part of the troubles prophesied by Jesus Christ.
Matthew 24:7 For nation shall rise against nation, and kingdom against kingdom: and there shall be famines, and pestilences, and earthquakes, in divers places.
Mark 13:8 For nation shall rise against nation, and kingdom against kingdom: and there shall be earthquakes in divers places, and there shall be famines and troubles: these are the beginnings of sorrows.
Luke 21:11 And great earthquakes shall be in divers places, and famines, and pestilences; and fearful sights and great signs shall there be from heaven.
These will continue until Christ returns.
An earthquake is prophesied at Jerusalem on his return, which will change the topography of Israel.
Zechariah 14:4 And his feet shall stand in that day upon the mount of Olives, which is before Jerusalem on the east, and the mount of Olives shall cleave in the midst thereof toward the east and toward the west, and there shall be a very great valley; and half of the mountain shall remove toward the north, and half of it toward the south.
Zechariah 14:10 All the land shall be turned as a plain from Geba to Rimmon south of Jerusalem: and it shall be lifted up, and inhabited in her place,
Earthquakes are a natural reminder that God intends to ‘shake the earth once more’ when he sends his son to judge the earth in righteousness and establish the kingdom of God.
This ‘earthquake’ will remove the corrupt governments and false religions devised by men. Justice will prevail and all men will be taught the truth.
Hebrews 12:26 Whose voice then shook the earth: but now he hath promised, saying, Yet once more I shake not the earth only, but also heaven. 27 And this word, Yet once more, signifieth the removing of those things that are shaken, as of things that are made, that those things which cannot be shaken may remain. 28 Wherefore we receiving a kingdom which cannot be moved, let us have grace, whereby we may serve God acceptably with reverence and godly fear: 29 For our God is a consuming fire.
This is what Paul preached on Mars hill.
Acts 17:30... God... now commandeth all men every where to repent: 31 Because he hath appointed a day, in the which he will judge the world in righteousness by that man whom he hath ordained; whereof he hath given assurance unto all men, in that he hath raised him from the dead.
We all die whether by earthquake, flood, war, famine, disease or natural causes. The only way that we can be saved is by resurrection from the dead when Christ returns. Only those who believe and obey the gospel can be saved.
Mark 16:15 And he said unto them, Go ye into all the world, and preach the gospel to every creature. 16 He that believeth and is baptized shall be saved...
I hope you have found this helpful.