Takafumi Horie denied that he had artificially inflated profits at the company by up to $45.3 million in order to boost Livedoor's share price.
"I've never done such things and I didn't order such things either. I regret this indictment," Mr Horie claimed at the hearing.
However, few observers believe that he has a leg to stand on considering that four other executives at the company have already pleaded guilty.
Further suspicions have been cast by fund manager Yoshiaki Murakami's recent confession that he engaged in insider trading in relation to Livedoor's controversial bid for Nippon Broadcasting System.
The case briefly rocked the Tokyo Stock Exchange earlier this year, when a raid on Livedoor company offices caused a huge sell-off of shares and the loss of some $327 billion from Japan's equity market.
If found guilty on fraud charges, Mr Horie could face up to five years in prison.