The broader Topix, however, added 0.06 percent to 1,596.12.

Investors were cautious as the United States and South Korea began long-planned joint military exercises on Monday, heightening tensions with North Korea which called the drills a "reckless" step toward nuclear conflict.

Volume of the broader market hit a three-month low of 1.315 billion shares, while turnover dropped to a four-month low of 1.714 trillion yen.

"Investors are staying on the sidelines amid geopolitical uncertainty. I don't think the market will see a sharp sell-off for now, but the mood is tense," said Isao Kubo, equity strategist at Nissay Asset Management.

Furthermore, Kubo said investors are holding their bets as they look for monetary policy insights from this week's meeting of global central banks at Jackson Hole, Wyoming, where Federal Reserve Chair Janet Yellen is due to speak.

Tokyo's non-ferrous metals sub-sector was up 1.1 percent with prices of copper having hit a near three-year peak and other industrial metals like zinc and nickel also buoyant.

Smelters Mitsubishi Materials Corp and DOWA Holdings Co added 1.6 percent and 2.5 percent, respectively. Toho Titanium climbed 2 percent.

Sumitomo Metal Mining rose as much as 4 percent to more than a 2-year high after the company said that it plans to install verification facilities for the mass production of high-purity nickel oxide powder to be used in fuel cell electrodes.

Demand for components related to fuel cell batteries are expected to increase along with the popularity of electric vehicles.

With iron ore prices soaring to multi-month highs the iron and steel subsector climbed 1.5 percent.

Major ferro-alloy maker Nippon Denko Co climbed 4.3 percent. Kogi Corp, a manufacturer of steel ingot moulds and steel rolling products, rose 2.3 percent. Komatsu Ltd , which produces iron ore-hauling trucks, rose 1.1 percent.

Elsewhere, real estate shares advanced, with Mitsui Fudosan rising 0.7 percent, while Mitsubishi Estate gained 0.6 percent. (Reporting by Ayai Tomisawa and Shinichi Saoshiro; Editing by Eric Meijer & Shri Navaratnam)