Tokyo stocks closed 0.35 percent lower on Monday after Crimea voted to break away from Ukraine and join Russia in a referendum described by the West as illegal.
The Nikkei 225-index, which sank 3.30 percent Friday, gave up 49.99 points to 14,277.67, while the Topix index of all first-section issues fell 0.84 percent, or 9.77 points, to 1,154.93.
"The Crimean vote was not totally unexpected, but it does nothing to defuse geopolitical tension in the region, which will continue to bear on global equities markets for the time being," said SMBC Nikko Securities general manager of equities Hiroichi Nishi.
Monex market analyst Toshiyuki Kanayama added that "despite all the selling we've seen lately, it's still too early to say that the market is oversold".
Crimea voted overwhelmingly Sunday to join Russia, further fuelling tensions in the worst crisis between Moscow and the West since the Cold War.
US President Barack Obama hinted at possible additional sanctions on Moscow, warning his Russian counterpart Vladimir Putin that Washington and its allies would "never" recognise Crimea's breakaway vote.
Japan has joined the chorus of criticism, saying it will cooperate with other Group of Seven world powers in dealing with the issue.
In share trading, Nikon fell 1.64 percent to 1,730 yen after China's government-controlled television broadcaster took aim at the Japanese camera maker as part of an annual campaign to stamp out service and quality problems that stifle spending in the country.
Toyota closed up 0.21 percent at 5,563 yen, as the world's biggest automaker suspended production at its two Indian auto assembly plants in response to threats against management and assembly-line stoppages, following failed efforts to reach a labour deal.
Mobile carrier SoftBank jumped 4.92 percent to 8,110 yen after Chinese e-commerce giant Alibaba Group said Sunday that it has decided to start the process for an initial public offering in the United States.
SoftBank owns about 37 percent of Alibaba, which is expected to raise more than $15 billion.
In forex markets, the dollar rose to 101.61 yen in Tokyo afternoon trade from 101.36 yen in New York Friday.
-- Dow Jones Newswires contributed to this article --