Most of those found in mass graves at the edge of Powazki military cemetery had been killed by a bullet to the neck, according to the IPN's forensic specialists, adding they would use DNA testing to establish their identities.
The bodies are suspected of belonging to victims of the post-war Stalinist reign of terror against Polish anti-Nazi and anti-Soviet partisans in the 1940s and 1950s.
The dig had been designed in part to locate anti-Nazi resistance heroes.
After the war, both men were accused of high treason and sentenced to death by Poland's communist authorities loyal to Soviet dictator Joseph Stalin. Their bodies were never found.
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The latest four-week dig followed the exhumation last year of 117 victims.
The institute believes that around 50,000 people were killed during the reign of terror in Poland, with many of the surviving family members still trying to locate their places of burial.