Out of the competing barrages of propaganda that have shrouded the 1950-53 Korean War, we are finally getting conclusive admissions that some of the worst atrocities, blamed at the time on the enemy, were in fact committed by our side - and we knew it. The commission is the legacy ofRoh Moo-hyun, the former human rights lawyer and political liberal who was South Korea's president for five years until February. It was set up in December 2005, and operates with a staff of 240 and a budget of $US19 million ($29.7 million) a year, with the daunting task of opening up a century of hidden history. This covers the Korean resistance to the 1910-45 Japanese annexation of the country, political oppression during the postwar occupation when the Americans and Russians set up rival regimes in their zones, the Korean War, and the succession ofright-wing and military dictatorships that lasted in South Korea until the late 1980s.

The massacres of civilians during the Korean War are the most shocking to read about. The commission is working through no less than 1200 cases, including about 215 incidents in which US and allied air forces strafed groups of refugees and other civilians. The victims total 100,000, which the commission says is a conservative estimate. One of the worst incidents preceded the Korean War, in 1948, when the new Syngman Rhee government installed in Seoul by the United States ordered its army to suppress a leftist revolt on Cheju Island. About 30,000 local people were gunned down. By early 1950 Rhee had about 30,000 alleged communists in his jails, and had about 300,000 suspected sympathisers enrolled in an official "re-education" movement known as the Bodo League. When Kim Il-sung's communist army attacked from the North in June that year, retreating South Korean forces executed the prisoners, along with many Bodo League members.

At Taejon, about 140kilometres south of Seoul, prisoners were shuttled out of the city's jail by the army and police, marched with hands bound to the edge of long trenches, made to lie down, and then shot with rifles. Their bodies were rolled in and covered. The death shuttle went on for days, as the North Koreans advanced, with up to 7000 prisoners executed, according to the commission. Two Australian military observers saw the prisoners being taken off as they passed through Taejon, and were under no illusions what was happening. A US Army major took photographs; they were sent to Washington within a month, but suppressed for half a century.

The American commander-in-chief, Douglas MacArthur, got a report about the killings, but there is no evidence that he tried to halt them, or investigate, according to a search of US archives by an Associated Pressteam under the veteran correspondent Charles Hanley. The massacre was blamed on the communists. Indeed, killings were authorised at lower level. Inthesouthern port-city of Busan, the US military adviser Lieutenant Colonel Rollins Emmerich recorded that a SouthKorean commander, Colonel Kim Chong-won, was planning to execute 3500 prisoners held for suspected communist sympathies. In a long-classified note, Emmerich said he persuaded him to hold off "until the situation was more critical". Busan was held by the Americans and South Koreans, but the picture emerging is that about 10,000 prisoners were eventually trucked out of the city and machine-gunned.

The litany of grim findings by the commission goes on: police and soldiers killed 160 civilians in Yeosu and Suncheon; another 600 killed in Cheondo; 140 in Ganghwa; 870 members of the Bodo League executed at Ulsan; 28 at Naju … There are massacres by North Koreans and local leftists as well: between 140 and 250 civilians around Dangjin in August and September 1950; between 70 and 120 at Gochang-myeon; 61 at Yangpyeong.

It does not stop with the end ofthe stalemated war in 1953. The commission has detailed human rights abuses committed right up to the early 1990s, including many cases of people being tortured, framed on false treason charges, jailed and, in some cases, executed. The findings are uncomfortable for Roh's conservative successor since February, Lee Myung-bak. At a recent ceremony in which the Supreme Court Chief Justice, Lee Yong-hoon, bowed his head and apologised for unjust court judgments in the past, Lee said the courts had to "guard against judicial populism".

Of course the findings reflect badly on the right, but even worse things will be unearthed if a similar inquest is ever held into North Korea's history. The exercise suggests an impressive maturity and sophistication in South Korea, a lesson for its bigger neighbours Japan and China.