A team of about 25 prosecutors and investigators from the Seoul Central District Prosecutors' Office seized digital files and documents from the National Intelligence Service (NIS) in the capital, Yonhap news agency said.
The agency's anti-North Korea psychological warfare team allegedly posted a slew of politically sensitive comments on the Internet against the opposition candidate to influence public opinion ahead of the December poll.
The raid follows the questioning of former NIS director Won Sei-Hoon on Monday in connection with the case.
Nobody at the Prosecutors' Office was immediately available to comment.
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Won reportedly denied the charges against him, claiming that the agency's anti-North Korea team was doing its job in countering Pyongyang's attempts to influence the election results.
Won is suspected of attempting to influence voter sentiment ahead of the presidential election in favour of the conservative ruling party candidate Park Geun-Hye, who narrowly defeated liberal rival Moon Jae-In to become South Korea's first female president.
Police wrapped up their four-month probe in March, accusing two NIS agents of taking part in the illegal political activities and handing the case to the prosecution for further investigation and possible indictment.