The ministry now has the authority to decide independently and without any input from municipal authorities where to locate cemeteries and how to maintain them.
The move is likely linked to Estonia's proposed reburial of Soviet soldiers resting near a Soviet monument in central Tallinn.
On Wednesday, the Estonian minister of defense said that the process of reburial would begin at the end of April, while Estonian mass media reported that the ministry had drafted a detailed plan on how the graves would be dug up, and how the remains of soldiers would be identified and reburied.
Reports also said the ministry had a plan on how to dismantle and move the Bronze Soldier statue.
Andrus Ansip, Estonia's prime minister, said Thursday that the process of exhumation and identification of remains would be conducted in line with international law.
"I declare that all work on the exhumation and identification of remains will be conducted in line with international law," Ansip said. "The Russian Embassy in Estonia has been informed of this. We are not going to use any wildcat methods."
Estonia's commission on wartime burials recommended March 13 removing the World War II Bronze Soldier statue, which is part of a Soviet-era memorial, from central Tallinn to a "quieter" military cemetery, in accordance with a new law passed in January.
A government security commission Tuesday discussed behind closed doors issues related to the removal of the monument and the reburial of Soviet soldiers' remains, but the subjects addressed were not made public.
The six-foot Bronze Soldier and other Soviet memorials have recently become rallying points for ethnic Russians, and following clashes with Estonian nationalists near the statues the authorities called for monuments "dividing society" to be removed.
Russia has accused Estonia of encouraging Nazism and discrimination against ethnic Russians, and even prompted a debate on possible energy sanctions against Estonia. Moscow has also called for international organizations to step in.
Some 50,000 Soviet troops perished in Estonia in 1944 fighting Nazi Germany. The Soviets regained control of the republic, which many Estonians call occupation. The bodies of the soldiers killed in action are buried at 450 cemeteries and memorials across the Baltic country.
The head of Russia's delegation to the Parliamentary Assembly of the Council of Europe (PACE) said Wednesday that Tallinn's decision to classify information about the Bronze Soldier's future means that Estonia is aware that the situation involving the monument is a disgrace for Europe.
"Estonian authorities must have begun to realize the obvious, that their actions regarding the monument are a disgrace for modern Europe," Konstantin Kosachev told RIA Novosti.
Russia's foreign minister said Wednesday he hopes the EU and NATO would persuade Estonia to change its mind on the issue.
"We hope the organizations Estonia strived to join, that is, NATO and the EU, will be true to their principles and will not allow this decision to be implemented," Sergei Lavrov told a Madrid news conference.
