The Nikkei 225 index at the Tokyo Stock Exchange fell 26.64 points to 8,348.27 on the first extended morning session. The Topix index of all first-section issues dropped 0.40 percent, or 2.90 points, to 717.08.
From Monday, the bourse lengthened the morning trade session by 30 minutes to 0230 GMT as it looks to boost trading activity while leaving unchanged the afternoon session, which closes at 0600 GMT.
The market continued to be weighed down by Europe's sovereign debt woes, said Kenichi Hirano operating officer at Tachibana Securities.
"The European situation remains unclear," he said, adding that Japan's unexpected trade deficit in October also hit sentiment.
Government data showed Japan logged a surprise trade deficit of 273.8 billion yen ($3.6 billion) in October as exports dropped off more steeply than expected with the yen high against the dollar and euro.
Exporters dragged the Nikkei index lower as volume remained weak. Toyota fell 2.57 percent to 2,385 yen and Honda was down 2.22 percent at 2,153 yen.
"There are simply few trading cues at the moment, with earnings season now effectively over, and the US 'supercommittee' (Joint Select Committee on Deficit Reduction) due to make its announcement on November 23," said Toshiyuki Kanayama, market analyst at Monex.
"Players are in wait-and-see mode," he told Dow Jones Newswires.
US lawmakers remained at odds over the weekend on a plan to reduce the nation's deficit.
A bipartisan "supercommittee" is racing against the Wednesday deadline to reach agreement. Failure would trigger mandatory cuts from January 2013, but that timeframe means Congress can wriggle out of the supposed ultimatum.
Shares in scandal-hit Olympus rallied 16 percent to 725 yen after a 16 percent fall on Friday.
"Those who are trading are more than likely day traders, or retail investors who buy and sell a name multiple times a day," a Japanese brokerage senior strategist said.
Uncertainty remains over the outcomes of various on-going investigations related to the company's admission this month that it had covered up investment losses going back to the 1990s.
The shares are around 70 percent down from their October 13 level, the day before the company ousted British chief executive Michael Woodford, who blew the whistle on payments made in a series of deals.
The euro fetched $1.3522 and 103.87 yen in Tokyo afternoon trade Monday, compared with $1.3519 and 104.00 yen in New York late Friday.
The dollar was at 76.80 yen, compared with 76.93 yen in New York and a post-war low of 75.32 yen at the end of last month.