The Nikkei 225 share index fell 0.69 percent to 23,127.75 by 02:07 GMT following the release of the GDP data, with healthcare and telecommunications shares pacing the decline.
The third straight quarter of declines knocked the size of real gross domestic product (GDP) to decade-low levels.
Personal consumption was significantly disrupted after people were asked to stay home and businesses, including restaurants and leisure facilities, were asked to close in a bid to stem the spread of the virus. Exports slid 18.5%, which was almost four times the first-quarter fall.
As a result, some economists are pessimistic about the recovery of the Japanese economy in the fall or later.
As for the July-September period, the Japanese economy is expected to grow at an annualized 13 percent, according to an average of predictions by 34 private-sector economists released on August 13 by the Japan Center for Economic Research, a nonprofit private research institute.
Japan has already deployed massive stimulus policies to cushion the blow from the health crisis, which hurt an economy already reeling from a sales tax hike a year ago - and the U.S.
Japan has seen a smaller coronavirus outbreak compared to some of the worst-hit countries, with infections approaching 55,000 and deaths at slightly under 1,100.
On April 7, a state of emergency was issued for the capital and six other prefectures and was thereafter expanded to cover the entire nation before being fully lifted on May 25.
Although Japan's second quarter contraction was not as bad as the comparable 32.9% plunge in the USA, it was a greater loss than its previous record - the 17.8% drop Japan suffered in the first quarter of 2009 during the global financial crisis.
While the economy has re-opened after the government lifted state of emergency measures in late May, a worrying resurgence in infections cloud the outlook for business and household spending. nd, the data showed.
Japan imposed looser restriction against the coronavirus and fared better than its industrial peers, said Naoya Oshikubo, senior economist at SuMi Trust.
Private consumption, which accounts for more than half of Japan's economy, fell 8.2% for the quarter, bigger than analysts' forecast of a 7.1% drop.
"We hope to do our utmost to push Japan's economy, which likely bottomed out in April and May, back to a recovery path driven by domestic demand", he told a news conference.