The reasons for the strength of the Japanese Yen have been its low external debt (most debt is owned by Japanese), large reserves and current account surplus.
However, Japan had a trade deficit in 2011, the first time since 1980 (See chart below courtesy of Trading Economics). The current account was still positive, but greatly reduced compared to previous years. If the trade deficit was to continue it could weaken the Yen, making it less of a safe heaven, and increase interest rates, which could snowball into a debt crisis and quickly deteriorate in a currency crisis.
Many people see Asian currencies, as being strong currencies. However, in 2011, with India debt to GDP over 90%, the Indian Rupee declined by up to 15% against the US dollar, although it recently rallied somewhat.
If you want to learn more about the Japanese Yen risk, check Mish Shedlock and Kyle Bass.