The benchmark Nikkei 225 index rose 14.15 points to 9,173.54, while the broader Topix index of all first-section shares was 0.62 percent, or 4.71 points, higher at 761.59.
Japan's biggest automakers -- which shut some or all of their China operations in the wake of violent weekend protests -- took a hit as the bitter tussle over a group of East China Sea islands spooked investors.
Nissan was down 2.3 percent at 721 yen and Honda was off 1.53 percent at 2,630 yen while Toyota dipped 0.9 percent in early trade but clawed up to 3,230 yen, or 0.46 percent higher.
A group of Japanese business leaders headed by Toyota's chairman said it may cancel a regular trip to China because of the territorial tussle.
Panasonic bucked an early downturn to trade up 1.24 percent at 571 yen after saying Monday it would temporarily shut some China operations.
Fast Retailing, operator of the Uniqlo cheap chic clothing chain, was down 5.42 percent to 17,770 yen as it announced the temporary shutdown of 42 outlets in China.
"There may be a kneejerk reaction, to what is happening in China with the protests, certainly," Toshiyuki Kanayama, market analyst at Monex, told Dow Jones Newswires.
"The extent of the impact on relevant companies' shares, however, will depend on how long the facilities are shut down, and how long the protests last."
Kanayama added that "it's difficult to conceive of this unrest dragging out over a prolonged period of time".
Widespread anti-Japanese demonstrations, some of them violent, have flared across China in recent days over the uninhabited archipelago -- known as Diaoyu by Beijing and Senkaku by Tokyo -- that is claimed by both nations but controlled by Japan.
The rocky outcrops are believed to sit atop vast mineral reserves.
China and Japan have close trade and business ties, with numerous Japanese companies investing in their larger neighbour and two-way trade totalling $342.9 billion last year, according to Chinese figures.
IOn the broader market dealers continued to find support after the US Federal Reserve announced last week new easing measures aimed at boosting the world's biggest economy -- a major market for Japanese products.
In currency trade the dollar eased to 78.57 yen from 78.70 yen late Monday in New York.
The euro bought $1.3109 compared with $1.3114, while trading at 103.00 yen, from 103.22 yen.
What the stars mean:
★ Poor ★ ★ Promising ★★★ Good ★★★★ Very good ★★★★★ Exceptional