The Strasbourg Court's verdict followed an appeal from the convict, Andrei Frolov, who complained about poor light, insufficient ventilation, inadequate heating in his cell as well as substandard food.
In 2006, the court considered 106 cases involving Russia, and only six were ruled in the state's favor, while the total number of complaints by Russian citizens reached 10,000. As a result, compensation worth more than 1.4 million euros will be paid from the Russian budget.
The Strasbourg Court has also failed to consider the most high-profile cases, including the complaint by the now bankrupt oil company Yukos against the Russian Federation filed in 2004.
Kononov, 84, a Russian World War II partisan, was convicted by Latvian authorities of war crimes for ordering the killing of several Nazi collaborators in 1944, while Latvia was occupied by German troops.
He filed an appeal to the court in Strasbourg in 2004, but the case has not yet begun.
While Kononov was in custody, his son and brother died, and his daughter was sent to a psychiatric hospital. In the fall of 2005, doctors diagnosed Kononov with a life-threatening illness.
Two other Russian WWII veterans, Nikolai Tess and Nikolai Larionov, who also lodged appeals with the court after being accused by Latvian authorities of genocide, died in 2006 and 2005, respectively, before the court could begin hearings.