But investors are still spooked, pushing the Topix index down 2.04 percent to 821.84 at lunch.
Exchange traded funds focusing on small companies and real estate or tracking the Topix index experienced the biggest inflows.
The Nikkei 225 average rose 5.7% to 9, 093.72, while the broader Topix index climbed 6.6% to 817.63 by the close.
FORBES: Japanese Stocks Rebound Despite Growing Radiation Fears
The broader Topix index fell 87.69 points, or 6.9%, to close 1, 188.34.
The fund has gained a 19.7% compound annualized return since its inception in June 1998, compared with 6.6% for a hedged version of Japan's topix index.
Along with the broad-based Topix index, the Nikkei is now nearly one-fifth below its peak for this year, in April, and more than three-fifths below its all-time high.
The changing dynamic of Japan's stock-market rally can be seen in the Topix index, whose 1, 669 stocks are divided into 33 subindexes, including shares of both exporters and domestically-focused companies, capturing a broader picture than the tech-heavy Nikkei.
The benchmark Nikkei 225, which has been reaching fresh lows almost every week recently, fell by 6.6%, to close below 10, 000 for the first time in over 17 years, while the Topix index, which covers a wider range of stocks, fell by 6.4% to below 1, 000.
Since the broad Topix stockmarket index slumped to a post-bubble low in October 1998, it has climbed by 70%.
News that a brash internet company, livedoor, was under investigation for market manipulation and accounting irregularities (see article) had sparked two days of widespread selling during which the benchmark Nikkei index and the broader Topix both fell by 5.7%.
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