The 225-issue Nikkei Stock Average closed 43.17 points, or 0.15 percent, lower from Friday at 29,025.46.
The broader Topix index of all First Section issues on the Tokyo Stock Exchange ended 4.70 points, or 0.23 percent, lower at 2,019.23.
Trading volume on the main section decreased to 1,084.98 million shares from Friday's 1,143.20 million shares.
Tokyo stocks fluctuated slightly in the morning and later stayed in the negative territory for the day, with the Nikkei index still above the 29,000-mark. In the past two trading days, the Nikkei gained almost 1,000 points and closed Friday at its highest closing since Sept. 30.
Yutaka Miura, a senior technical analyst at Mizuho Securities Co., said, "Many investors aim to secure profits when the Nikkei moves above the 29,000 line," adding that concerns over rising oil prices and the full-year earnings outlook from domestic companies also dragged down the market performance.
Oil prices kept their upward trend, with benchmark West Texas Intermediate crude futures extending gains in after-hours trading after hitting a seven-year high on Friday in the New York market.
Higher oil prices could lift the input costs of many businesses, resulting in lower profits and possibly slowing the pace of the global economic recovery.
Investors would pay close attention to the release of earnings for the April-September period later this month to evaluate the impact of oil prices hikes on Japanese firms, brokers said.
Japanese Prime Minister Fumio Kishida said on Monday after an emergency meeting of cabinet members that his government would work with the International Energy Agency to urge oil-producing countries to increase output as well as to "swiftly take appropriate action" for industries that might be negatively affected.
By the close of play, pharmaceutical, farm and fishery, and precision instrument issues were major decliners. Despite indexes ended with a lower closing, advancing shares outnumbered declining ones 1,124 to 985, while 75 finished unchanged.
Some electronic component makers and chip-related issues declined after a surge last week. Industrial robot producer Yaskawa Electric fell 1.9 percent, and chip equipment maker Screen Holdings decreased 0.7 percent.
Airlines faced selling amid ongoing concerns that higher crude oil prices could raise their fuel costs, with both Japan Airlines and ANA Holdings ending down 0.2 percent.