On the surface, it seems like the Japanese government has repeatedly acknowledged its crimes during World War II. See List of war apology statements issued by Japan.
They have indeed. They have also repeatedly retracted those apologies. The strongest apologies have come from lower level officials. Even an apology by the prime minister is really like John Boehner apologizing for America. An clear and unambiguous apology by the emperor would carry far more weight.
Not exactly. An apology from a prime minister (and there are quite a few on the linked Wikipedia page) is like an apology from the President of the US. Prime Minister=head of the government. If you want one from the head of state, however, the emperor, then how about this one on the same page?
October 8, 1996: Emperor Akihito said in a speech at a dinner with the South Korean president, Kim Dae Jung: "There was a period when our nation brought to bear great sufferings upon the people of the Korean Peninsula." "The deep sorrow that I feel over this will never be forgotten".