The yen neared a one-week high versus the dollar, rising 0.2pc to 108.295.
Against the Australian dollar it soared to its highest since a January flash crash.
The Aussie, seen as a barometer of global risk sentiment, was also hurt by jobs data taken as a green light for an early interest rate cut.
With growing doubts about any improvement in what US President Trump called "testy" trade relations between Washington and Beijing before the G20 summit, investors sold stocks and looked for safety.
Adding to the unease, protests broke out again in Hong Kong over a planned extradition law with mainland China, while oil prices surged after reports of a tanker on fire in the Gulf of Oman followed earlier sabotage attacks on vessels near the Fujairah emirate.
"The risk aversion and falling stock markets are supporting the yen as usual," said Bart Wakabayashi, Tokyo branch manager for State Street Bank and Trust.
"The Australian dollar's underperformance is also a booster for the yen."
The Aussie was down 0.3pc against the US currency at $0.6911 while against the yen it dropped 0.6pc to 74.80 yen.
MUFG analysts noted that markets were pricing in a 65pc chance of an Australian rate cut in July, and a more than 80pc chance of one by August and September.
Australian government bond yields slid to record lows.
"Overall this should keep downward pressure on the Aussie going forward," they wrote in a note to clients.
The US dollar index, which measures the currency against a basket of rivals, inched lower to 96.929, while the euro rose 0.1pc to $1.1297 in a quiet start to the trading day in London.
The dollar index had dropped to 96.459 on Monday, its lowest since late March, following a sharp decline in long-term US Treasury yields. They fell to near two-year lows last week after a soft US jobs report bolstered expectations of an interest rate cut by the Federal Reserve.
Sterling slipped on Wednesday as British lawmakers defeated an attempt led by the opposition Labour Party to try to block a no-deal Brexit.
Uncertainty over Brexit, and the Conservative party leadership contest, are keeping the pound under pressure, although the currency remains firmly within recent trading ranges.
Early on Thursday it slipped 0.2pc to $1.2667.