The Nikkei 225 was down by 0.8 percent to close at 23,783.72, while the Topix index slipped by 0.47 percent to 1,792.65.
In South Korea, the Kospi slid 0.31 percent to close at 2,267.52, as shares of heavyweight Samsung Electronics ended largely flat despite earlier saying that its third-quarter operating profit was likely to have risen to a record high.
Meanwhile, Hong Kong's Hang Seng index slid by 0.19 percent to close at 26,572.57, with computer maker Lenovo's stock dropping by 15.1 percent.
Down Under, the ASX 200 bucked the overall trend to edge up 0.15 percent to close at 6,185.5, with the energy sector also higher by 0.15 percent. Oil and gas explorer Beach Energy, which had earlier announced the sale of a 40 percent stake in its Victorian Otway gas assets and trimmed its earnings guidance for fiscal year 2019, saw its stock fall by 3.65 percent.
China's markets were closed for the Golden Week holiday.
Stocks of Apple suppliers in Asia fall
Wall Street moves overnight
Pence takes aim at China
The vice president's comments follow Trump's own accusations of Beijing attempting to meddle in the upcoming midterm elections.
Neither Trump nor Pence has provided hard evidence of the alleged meddling, while China rejected the president's claims from late September.
Currencies and oil
The Japanese yen saw a slight gain at 113.80 against the dollar, while the Australian dollar declined 0.21 percent at $0.7057, as of 3:34 p.m. HK/SIN.
In oil markets, prices saw extended gains in the afternoon of Asian trade. As of 3:35 p.m. HK/SIN, the global benchmark Brent crude futures contract climbed 0.54 percent to $85.04 per barrel, while the U.S crude futures contract gained 0.69 percent to $74.84 per barrel.
— CNBC's Fred Imbert and Reuters contributed to this report.