Tokyo's key Nikkei index lost more than 1.5% today following an unprecedented 10-day break to mark the ascension of a new emperor.
The index tracked global declines after US President Donald Trump threatened new tariffs on Chinese goods.
The benchmark Nikkei 225 index fell 335 points to close at 21,924.
Other Asian shares staggered up from five-week lows but remained fragile.
This comes after US President Donald Trump's latest threat to raise tariffs on Chinese goods shocked financial markets and fueled worries that trade talks may be derailed.
MSCI's broadest index of Asia-Pacific shares outside Japan rose 0.5%, erasing earlier losses. The inde had tumbled 2% yesterday after Trump unexpectedly jacked up pressure on Beijing in the midst of trade negotiations.
Chinese shares rose after their worst drop in more than three years yesterday. The benchmark Shanghai Composite advanced 0.6%, while the blue-chip CSI 300 climbed 1%. Hong Kong's Hang Seng was up 0.7%.
Trump tweeted on Sunday that he would raise tariffs on $200 billion worth of Chinese goods to 25% from 10% by the end of the week and would "soon" target the remaining Chinese imports with tariffs.
Analysts said that stocks have entered a new down trend, as investors had growing doubts over whether the US and China would cut a deal on trade any time soon.