An exchange official said the exchange would resume trading Livedoor stock later on Wednesday after the suspension earlier in the day.
Prosecutors raided the offices of the company on Monday, and Kyodo News agency reported on Wednesday that the authorities had opened a second investigation into the company.
Neither Livedoor nor the Tokyo prosecutors office could confirm the report.
Takafumi Horie, the company's 33-year-old chief executive, on Tuesday denied any wrongdoing, adding that the company is co-operating with prosecutors and also conducting its own investigation.
The national daily Yomiuri Shimbun reported on Wednesday that Livedoor is suspected of concealing a ¥1 billion ($8.7 million) deficit for the full-year results ending September 2004.
Livedoor is suspected of transferring about ¥2.4 billion in profits from three affiliates so that it could be book a surplus of about ¥1.4 billion for that year, the Yomiuri reported.
The company's stock fell the maximum amount allowed on Tuesday to ¥596, down 14.4% or the ¥100 limit, from Monday.
The raid rattled Japan's stock market on Tuesday, with the
Nikkei 225 index plunging 462.08 points, or 2.8%, its biggest one-day loss since May 2004.
The Nikkei opened lower on Wednesday, down 80.31 points, or