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The Nikkei closed down 0.3% at 12,314.81 points after earlier rising as high as 12,461.97, its strongest level since early September 2008.
Weakness in the yen boosted the Nikkei in early trade, but it later surrendered those gains as signs of overheating began to emerge.
The benchmark had risen more than 8% over the past eight sessions through Monday, its longest winning streak since July 2009 and putting it in technically overbought territory.
"Some stocks' prices have doubled over the past months ... profit-taking is natural at this point," said Fujio Ando, senior managing director at Chibagin Securities.
Exporters and financials lost ground, with Toyota Motor Corp falling 0.8%, Sony Corp shedding 2.0% and Toshiba Corp dropping 1.5%.
Among financials, Mizuho Financial Group fell 0.9% to 213 yen and Sumitomo Mitsui Financial Group dropped 1.0%.
But analysts said that the Nikkei is still on a rising trend on hopes for more aggressive policy easing by the central bank, and while a short-term correction is possible, the index could head towards 12,500 in the coming month.
"Positive views on the US economy and easing hopes in Japan are major catalysts, and they haven't changed," said Hiroichi Nishi, an assistant general manager at SMBC Nikko Securities.
Buying on the dips
While some analysts point out that the Japanese market is overheated after the recent rally, some investors have waited to scoop up such laggards as trading houses.
The wholesales subindex was one of the gainers on the board, with Marubeni Corp rising 1.0% and Mitsubishi Corp gaining 1.2%.
"Stocks that have fallen behind the overall rises attracted buying today," said Eiji Kinouchi, senior strategist at Daiwa Securities.
Among Tuesday's gainers, shares in drilling companies also jumped after news that a government-led team has successfully extracted methane hydrate gas from the seabed for the first time in the world, off the coast of Japan.
Japan Drilling Co Ltd shot up 18.3% and Modec Inc jumped 7.1%.
"Retail investors showed interest in these shares, but those gains will probably fade soon as their bottom lines won't dramatically rise just because of the news," Chibagin's Ando said.
Nippon Steel & Sumitomo Metal Corp surged 4.4% after the company said it would halt operations at a blast furnace at a major steel mill in a bid to cut costs and resolve overcapacity. The share rise helped the steel subindex become the top sectoral gainer, gaining 2.0%.
