The yield on the current 10-year JGBs dropped 0.5 basis point to 0.250 percent, hitting a one-year low of 0.245 percent at one point. The five-year bonds were traded at 0.025 percent .
The yield fell below 0.03 percent, which had been a strong yield resistance for the last couple of months.
The 10-year JGB futures hit an all-time high of 149.20.
Although many investors had been cautious about bidding up JGBs further beyond current low yield levels, a string of worrying news on the global economy and geopolitics gave them the push.
China's central bank set the yuan at a much weaker level than Tuesday's close, a move that sparked fresh speculation that Beijing wants a weaker yuan as its economy loses momentum.
Growth in China's services sector slowed to its weakest in 17 months in December, a private survey showed, stoking further worries about the strength of the economy.
North Korea said it successfully tested a miniaturised hydrogen nuclear device on Wednesday, claiming a significant advance in the country's strike capability.