Yevgeny Savenko, 85, is accused of ordering nine people to die and condemning four dozen others as enemies of the Soviet regime while he served as a top KGB official in Liepaja in the 1940s.
Supporters of Savenko, a Russian citizen, helped fill the court room in the port town of 90,000 to standing room only.
Arguments reportedly broke out between Savenko supporters and others in the courtroom, including an alleged victim in Liepaja to testify against Savenko.
Other alleged victims are expected to trickle into Liepaja this week to testify.
If convicted, Savenko faces possible life in prison.
"I am to blame that I did not quit the KGB earlier," he told the court on the opening day of the trial. "But as an officer I had sworn allegiance and felt responsibility."
The Prosecutor's Office argues that Savenko's crimes took place during both Soviet occupations.
From 1940 through 1941 Savenko was the senior investigator at the KGB's Riga office and allegedly set in motion a number deportations and killings.
In 1944 Savenko became deputy head of Liepaja's KGB office and director of a department aimed at stamping out Latvia's fledgling nationalist forces that hung on in the early years after World War II.
During the trial Savenko called them "gangs" outfitted with "common thieves," according to reports.
Criminal prosecutors opened a case against Savenko in May 1998 and arrested him last October in Liepaja, where he and his wife still live.
Russian officials have slammed Latvia in recent weeks for the prosecution of Soviet war criminals, especially Vasily Kononovs, a "Red Partisan" who fought Nazis and killed "traitors".
Former Russian President Boris Yeltsin cited the Kononovs case as part of the reason he turned down a medal awarded him last month by the Latvian government for his role in the country's independence.
"There was support at the highest level of government (for Kononovs)," said Vladimir Ivanov, a spokesman at the Russian embassy in Riga.
Latvia has been vigilant in prosecuting Soviet war crimes in recent years and now nationalist groups are asking the parliament here to go a step further.
A letter calling on heads of government from all three Baltic States to draw up a shared statement on the Soviet occupation that includes calls to demand compensation from Moscow for victims of Soviet oppression.
"The world has to learn the historical truth," the letter reads. "To become able to distinguish between the attackers — occupants — and those who defended their fatherland."
The letter was signed by the Kurzeme District Club of Repressed Persons, the Daugavas Vanagi National Union of War Veterans, the National Soldiers Society and the Latvian National Partisans Association.
Meanwhile, Latvia continues to draw criticism from abroad over their failure to prosecute alleged war criminal that fought for the Nazis, particularly the case of Konrads Kalejs who is believed to be living in Australia.
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