The 225-issue Nikkei Stock Average closed 182.80 points, or 0.61 percent, lower from Thursday at 29,611.57.
The broader Topix index of all First Section issues on the Tokyo Stock Exchange ended 14.14 points, or 0.69 percent, lower at 2,041.42.
Trading volume on the main section decreased to 1,266.64 million shares from Thursday's 1,482.77 million shares.
Tokyo stocks opened lower in the morning as gains were locked in after the U.S. Federal Reserve policy meeting ended without any surprises for the market, and both Nikkei and Topix indexes stayed in negative territory for the rest of the day.
Kenji Abe, the chief strategist at Daiwa Securities Co., said, "The market took a breather after advancing on the outcomes of the lower house election and the FOMC."
The U.S. dollar against the Japanese yen was under pressure in the upper 113 yen range as a decline in U.S. Treasury yields would possibly narrow the interest rate gap between the United States and Japan, dealers said.
By the close of play, marine transportation, iron and steel, and warehousing and harbor transportation service companies led the downtrend. Declining issues outnumbered advancing ones 1,591 to 540, while 52 finished unchanged.
Automakers declined on the strong yen, with Honda Motor losing 3.1 percent and Subaru slipping 2.6 percent. Their falls came before releasing their earnings reports for the fiscal first half through September.
Honda on Friday trimmed its net profit outlook for the current business year to 555 billion yen (4.9 billion U.S. dollars) due to output cuts.
Toyota Motor also ended down 1.4 percent a day after its latest released earnings forecast for the year through March 2022, shown concerns over recent rises in raw material cost, failed to meet the market expectations.
Bucking the downward trend, renewable energy company Renova surged 15.1 percent as many countries pledged to stop the use of coal during a UN climate summit being held in Scotland.