The police have installed floodlights on the upper levels of buildings and are preventing people from entering the square where the memorial stood until Friday.
The site is likely to be closed May 9 when Europe celebrates VE Day.
Apart from the 13 soldiers buried in 1947 under the Bronze Soldier, about 50,000 Soviet soldiers are believed to be buried in 450 WWII burials across Estonia.
There were violent clashes between protesters and police as crowds gathered in Tallinn after Estonian police cordoned off the area around the Soviet World War II memorial, which was dismantled and removed early Friday. As a result of the clashes in the central streets of Tallinn, one man aged 19-20 died, 60 injured, and over 500 detained. The deceased was a Russian national.
Estonia has said the Bronze Soldier 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.
European institutions have made no comment on the dismantling of the monument in EU member Estonia so far.