Youth movements have been holding rallies near the Estonian embassy in Moscow demanding that a World War Two monument the Estonian authorities removed from Tallinn's center Friday be returned to the Tynismyagi square.
"The life and health of embassy employees, as well as of their family members, are in danger," the note reads.
The ministry demands that the Russian authorities fulfill their direct obligations under the Vienna convention to ensure the security of Estonian embassy employees and their free movement, which has been impossible due to rallies.
During the night Friday, the Estonian government made the decision to remove the Bronze Soldier statue from Tynismyagi square, in central Tallinn, which led to clashes between police and a crowd of protesters that had gathered in the square to protest the government decision.
Estonian police have detained nearly 1,000 people since April 27. One man, a Russian national, was killed in the clashes, and more than 150 were injured.
The Russian embassy in Estonia said a delegation of the lower house of Russia's parliament arrived in Tallinn to get familiarized with the situation over Estonian authorities' decision to move the monument.
Estonia has said the Bronze Statue and other Soviet monuments - rallying points for ethnic Russians and places of their clashes with Estonian nationalists - "divide society," and the central square is not a proper burial place.
Estonian authorities see the monument as a sign of Soviet occupation but Russians revere it as a symbol of war heroism.
The Estonian parliament earlier passed laws allowing the removal of Soviet monuments and the exhumation of Soviet soldiers, claiming that monuments that encourage social divisions must be removed.
Russia has repeatedly drawn the European Union's attention to attempts by Estonia, which declared its independence from the Soviet Union in the early 1990s and joined NATO and the EU in 2004, to glorify Nazi Germany, including allowing parades by former Nazi SS fighters.
Moscow has also harshly criticized Estonia's discriminatory policies with respect to ethnic Russians and their descendents, who moved to the republic following its annexation by the Soviet Union in 1940.
Moscow Mayor Yury Luzhkov and the legislature of the Leningrad Region surrounding Russia's second-largest city, St. Petersburg, have called on all government institutions and government-run organizations to freeze financial and economic transactions with Estonia, and on all Russians to boycott Estonian goods.
Flamboyant Russian nationalist Vladimir Zhirinovsky, deputy speaker of the lower house, has offered to fund a replica of the Tallinn memorial to be installed across the street from the Estonian embassy in Moscow.
