The 17-nation currency bought $1.2287 and 96.60 yen in Tokyo afternoon trade, from $1.2280 and 96.75 yen in New York late Wednesday.
The dollar slipped to 78.61 yen from 78.78 yen.
It was the greenback's first dip below 78.70 yen in about a month, with short-term speculators selling the unit to trim losses, dealers said.
"The declines are not news-driven, and large commercial sales aren't seen," said a currency manager at a major Japanese bank.
The US currency also lost ground against the commodity-driven Australian dollar, which bought US$1.0392 from US$1.0308 Wednesday afternoon.
"However, the dollar has not weakened against all major currencies. The euro has its own problems and has not been bought," Osao Iizuka, head of FX trading at Sumitomo Mitsui Trust Bank, told Dow Jones Newswires.
The market had also started to price in another possible round of easing by the US Federal Reserve, which could drive down the dollar, analysts said.
Merkel said Wednesday she was "optimistic" but could not be certain that the European project would work, in comments that cast doubt on plans for tighter European integration and weighed on the single currency.
Also Wednesday, the International Monetary Fund warned that the eurozone was in "critical" danger, and needed to make speedy moves towards a banking union and some form of pooled debt.
The US dollar was mixed against other Asia-Pacific currencies.
It weakened to Sg$1.2569 from Sg$1.2598 on Wednesday and to 1,138.50 South Korean won from 1,139.90 won.
The dollar firmed to 41.72 Philippine pesos from 41.63 pesos, to 55.28 Indian rupees from 55.19 rupees, and to 9,470.00 Indonesian rupiah from 9,465.00, while it was flat at 31.66 Thai baht and Tw$29.97.
The Chinese yuan bought 12.34 yen from 12.37 yen.