The incident has sparked a fierce political dispute ahead of the June 13 local elections, as Rep. Kim Kyoung-soo of the ruling Democratic Party, a close aide to President Moon Jae-in, is known to have been in contact with a key suspect for years.
Opposition parties have submitted bills calling for an independent counsel to investigate the scandal.
The Seoul Metropolitan Police Agency raided the publishing firm in Paju, north of Seoul, the district tax office and an accounting firm in Gangnam to confiscate evidence, the agency said.
They plan to track down where the sources of the funds that were used in the scheme to manipulate the Internet comments came from and how the money was spent, police said.
Tuesday's raid came after police obtained a testimony from a worker of the publishing firm that he destroyed financial documents as soon as he sent them to the accounting firm.
"We are looking into the evidence to see if there were possible transactions of illegal funds between the suspects and others who are involved in the case," a police official said.
Police are investigating the suspected rigging of Internet news comments by the three-member group, headed by a 48-year-old surnamed Kim, who has been charged over the scandal.
Kim, who goes by the nickname Druking, is alleged to have used a software program to jack up the number of clicks in support of comments critical of the president on certain news articles.
Kim, once an ardent supporter of Moon, faces suspicion that he turned hostile against the government after the lawmaker refused his request to appoint his acquaintance to a consul-general position.
Police also said they plan to bring in an aide of the lawmaker for questioning. The aide is suspected of receiving 5 million won ($4,640) from one of Druking's associates last year and returning the money after Kim was arrested.(Yonhap)