The record fine against Livedoor surpassed the 200m yen ($1.7m) penalty imposed in 2005 on Seibu Railway for falsifying financial statements, according to the government's Financial Services Agency.
In a separate session earlier on Friday, Taishin Hisano, an accountant at Livedoor, was sentenced to 10 months in prison, while Motoshi Kobayashi, his supervisor, received one year in prison suspended for four years, a court official said.
Japan's Kyodo news agency reported that it was the first time in Japan that a certified accountant had received a prison term in a court case involving securities laws violations. Both accountants pleaded not guilty.
The latest convictions bring the number of people convicted in the Livedoor case to seven, beginning with Takafumi Horie, the former chief executive, who was sentenced to two and half years in prison last Friday.
The tough fines and prison terms given to those at the center of the scandal come as part of a growing effort to crack down on companies testing what are still grey areas in regulation on stock trading in Japan.
In the past, executives charged with tampering with earnings reports, even at companies bigger than Livedoor, had generally avoided prison terms and got suspended sentences.
On Thursday four former Livedoor executives were found guilty of securities laws violations with three of the former officials being given suspended sentences and Ryoji Miyauchi, Livedoor's former chief financial officer, sentenced to 20 months in prison.
The executives are accused of setting up a number of funds that prosecutors alleged were "dummy" entities to do stock swaps and other stock trading.
Prosecutors said the complex set of schemes fabricated 5bn yen ($42.5m) in profit.
The Livedoor scandal broke in January 2006, when prosecutors arrested Horie and other top executives, triggering a sell-off on the Tokyo stock market and prompting calls for clearer laws about stock trading.
Livedoor was delisted from a Tokyo exchange for startups but has been trying to rebuild its business under new management.