Agents from a special team of South Korean prosecutors investigating Samsung Group raided the conglomerate's headquarters building in Seoul, Yonhap news agency reported on Tuesday.
The move comes after prosecutors searched an office of its chairman, Lee Kun-hee, and homes of other executives on Monday but were seen leaving the premises with only a small volume of documents.
South Korea launched last week a special probe into the group on suspicions the country's largest conglomerate bribed public officials to squash investigations into its management practices.
Officials at the special counsel office could not be reached for comment. An official at Samsung's group headquarters said its offices were being raided but the move did not appear to involve the offices of Samsung Electronics in the same building.
South Korea's parliament approved the special counsel in November in response to allegations made by a former top legal executive at the group who said it used its subsidiaries to help create a slush fund.
Samsung has denied the accusations, calling them groundless, and issued detailed rebuttals of the claims made by the former legal executive Kim Yong-cheol.
South Korean prosecutors had conducted a separate probe following Kim's accusations. Kim, who waited about three years after leaving Samsung to make the charges in late 2007, said the company bribed members of the prosecution.
In December, soon after Kim's allegations, the country's financial watchdogs said a bank and a brokerage had violated banking rules when handling accounts set up for the Samsung Group.
Kim said Samsung set up the accounts in employees' names as a way to hide money for slush funds.
Best known for Samsung Electronics, the world's top maker of LCD screens and memory chips, the Samsung Group wields enormous power in South Korea.
The special counsel, which began its probe last week, has about 100 days to conduct its investigation.