The speech coincided with legal wrangles over the issuing of a warrant for the arrest of Konrads Kalejs, an 87-year-old ethnic Latvian currently living in Australia and suspected of Nazi war crimes.
Vike-Freiberga backed such prosecutions.
"We must set about understanding our past and, yes, pursuing those who are still alive and have not been punished for crimes they committed so long ago," she told the audience at the University of Latvia in Riga.
Whilst acknowledging that Latvian participation in war crimes was sometimes under duress, the president also spoke of Latvia's responsibility.
"It is our shame that this anti-human event took place on our soil and with the collaboration of some of our own citizens," she said.
The pursuit of historical truth means separating documented fact from interpretations, and emotions from reason, she said.
The aim of the conference, entitled Problems in Holocaust Studies in Latvia, was to promote the study of the Holocaust and increase knowledge of the subject in society. Contributors included experts from Latvia, the United States, Germany, Russia, Sweden, Finland, Israel, Lithuania and Great Britain. It was the latest in a series of events organized by a commission established last year to examine Latvia's past.
The prosecutor general's application for a warrant for Kalejs' arrest has been returned to a second judge in Riga District Court after a previous judge rejected the initial application and an appeal was made to the district court.