Striking South Korean journalists at public broadcaster KBS posted the findings online Thursday, Yonhap News Agency reported.
The report said 2,619 cases of government reports from an ethics team from the prime minister's office show the team, designed to ensure public officials are not involved in corruption, collected information on government officials as well as civilians deemed critical of the government, including union labor leaders and reporters.
The report said the surveillance targeted more than 2,600 people and some of the documents said "BH ordered," which many say they believe stands for the Blue House, or presidential office, The Korea Herald said.
Critics blamed President Lee Myung-bak after the report, which comes less than two weeks before April 11 parliamentary elections.
"The reported truth about illegal surveillance is shocking," said Han Myeong-sook, the leader of the main opposition party, the Democratic Union Party.
Han called on Lee to disclose whether he was involved in the surveillance and to punish those responsible.
Ranking DUP lawmaker Park Young-sun said the country should consider discussing Lee's possible resignation.
"We have defined this case as a Korean version of the Watergate scandal," Park said.
Lee Sang-il, a spokesman for the ruling Saenuri Party, said of the alleged spying: "If this is true, this is an infringement on human rights and destruction of democracy. The prosecution should sternly punish those responsible."
The prime minister's office said the documents were among evidence prosecutors seized and turned over to a court in 2010.
Yonhap said prosecutors had reopened an investigation this month into government surveillance after an official said the president's office attempted to cover up illegal spying.
After an earlier investigation, seven officials were indicted for illegal surveillance of a businessman who posted online a video clip criticizing the Lee government for resuming U.S. beef imports in 2008. The investigation concluded the president's office was not involved.