The Nikkei average rose 0.49 percent to 36,380.17 while the broader Topix index closed 0.38 percent higher at 2,565.37. The Bank of Japan meets later this week but no move is expected on rates.
Daiichi Sankyo fell 1.5 percent despite reporting positive initial findings from the dose escalation phase of the Phase I trial of its investigational antibody-drug conjugate (ADC) DS-9606 for treating advanced solid tumors.
Japan's core machinery orders declined unexpectedly in July, data from Cabinet Office showed on Wednesday.
Core machinery orders that exclude volatile orders for ships and electric utilities, fell 0.1 percent on a monthly basis, confounding expectations for an increase of 0.4 percent. This followed June's 2.1 percent growth.
On a yearly basis, core machinery orders surged 8.7 percent, in contrast to the 1.7 percent drop posted in June.
Another official data showed that Japan's exports growth eased to 5.6 percent in August, from 10.2 percent rise in July. At the same time, imports climbed only 2.3 percent after a 16.6 percent surge.
Consequently, the trade balance showed a shortfall of JPY 695.3 billion compared to a JPY 940.1 billion deficit seen a year ago.
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