The benchmark Nikkei 225 index edged up 0.12 percent, or 26.66 points, to 21,803.95. The broader Topix index was up just 0.02 percent or 0.39 points to end the session at 1,743.60.

The Thursday session opened lower, tracking falls on Wall Street amid rising worries that US President Donald Trump administration's policies could ignite a global trade war.

Daiwa Securities senior strategist Ishiguro Hideyuki said "political risks both in Japan and the US are a burden", but bargain-hunting activities for individual shares were supporting the market.

The US announced Wednesday it was taking action at the World Trade Organization against Indian export subsidies.

The move comes as the White House is also considering slapping tariffs on billions of dollars in Chinese imports, particularly in the tech and telecommunications sector, in response to alleged improper practices involving American intellectual property.

At home, Japanese Prime Minister Shinzo Abe's government has faced mounting pressure in recent days over the 2016 sale of state-owned land to one of his supporters at a price well below market value.

Earlier this week, Japan's finance minister admitted that official papers related to the sale had been altered, adding fuel to the simmering fire.

Foreign investors are particularly sensitive to geopolitical risks, analysts say.

The dollar fetched 106.00 yen in late Tokyo trading time, down from 106.32 yen in New York and 106.56 yen in Tokyo Wednesday.

Sony closed 0.85 percent higher at 5,446 yen and Uniqlo casual wear operator Fast Retailing closed up 0.30 percent at 42,190 yen.

Automakers were mixed, with Honda edging up 0.18 percent to 3,694 yen while Toyota closing down 0.11 percent at 6,931 yen and Nissan down 0.31 percent at 1,122 yen.