De Zwaan had previously apologized to victims' relatives during a visit to Rawagede in 2011, after an earlier court ruling ordered the Netherlands to give each of those 10 surviving widows the same amount in compensation.
In his speech at the Dutch Embassy in Jakarta, which was meant as a more general apology for all war atrocities, the ambassador said the violence claimed many innocent victims on both sides and resulted in suffering that is still felt today.
"The Dutch government hopes that this apology will help close a difficult chapter for those whose lives were impacted so directly by the violent excesses that took place between 1945 and 1949," he said.
Indonesia's presidential office declined to comment, referring queries to the Foreign Ministry. It did not immediately respond to requests for comment.
Indonesia declared its independence from Dutch colonial rule on Aug. 17, 1945, but the Netherlands refused to acknowledge it and fought unsuccessfully to maintain control of the lucrative Asian outpost. It finally recognized the country as an independent nation in 1949.
Indonesian authorities claim some 40,000 people were killed during the operation, while most Dutch historians estimate the dead at about 1,500.
A 1968 Dutch report acknowledged "violent excesses" in Indonesia but argued that Dutch troops were conducting a "police action" often incited by guerrilla warfare and terror attacks. The Dutch government has never prosecuted any soldiers for the killings despite a U.N. report condemning the attack as "deliberate and ruthless" as early as 1948.
De Zwaan was scheduled to travel to South Sulawesi next week to meet directly with some of the surviving widows who were too weak due to their age to attend Thursday's event.
None of the relatives attending the ceremony agreed to speak to speak to the press.
