Experts have found the remains from World War II in various burial sites around the village of Borky in the Pskov region.
Remains of up to 50 victims with multiple gunshot wounds were found during the first exhumation, and many more are expected to be discovered.
The hunt began after the work of local teacher and ethnographer Olga Petrova in her research into the genocide committed during the war in this region.
It is believed that women, children and the elderly were brought in trucks to be executed.
The findings led to the opening of an official criminal case for genocide by the Russian commission of inquiry.
Ms Petrova said: “There are memories of Raisa Gorokhova, who was a child at the time.
“In one of the many covered trucks [which took people to be shot], she made out the face of a teacher, Maria Voitsekhovskaya.
“She had a three-year-old son. And she shouted: ‘Good people, they are taking us to Borki for execution. Help us’. “
A video by Vesti Pskov shows investigative committee officers digging up the human remains.
Igor Neofitov, head of the Pamyat (“Memory”) research unit, said: “The depth of the burial is not yet known.
“But it is clear that people have been shot dead here on several occasions.
“There are summer and winter shoes for the murdered, including children. “
He added: “While the search operations are ongoing, we still do not fully understand the scale of the disaster.
“The first location has already been found, and it is clear that the work here can last for months, not weeks. “
The Germans occupied this area on July 15, 1941, and it is estimated that up to 20,000 civilians were shot dead.
A number of possible mass grave locations are currently under study.
Classified documents will be made available to investigators, but evidence suggests that the victims were moved to the site from the Pskov and Smolensk regions.
Elena Tsunaeva, of the Russian Research Movement, said: “After the war ended, an investigation was carried out.
“But not everyone was punished then.
“Nonetheless, the now declassified archival documents and research results will help restore a comprehensive list of those who were victims of genocide during the years of war. “