Dozens of police faced the 100 protesters at the Bronze Soldier monument as workers erected a tent over the memorial to shield the excavations from public view. Some protesters shouted "Estonia is a disgrace," and one was detained after trying to jump the police barrier.
Three other protesters were detained earlier Thursday after locking themselves in a car and refusing to obey police orders, police spokeswoman Julia Garanza said. Officers smashed the windows of the car.
Estonia's government intends to relocate the Soviet grave - which is believed to contain the remains of 14 soldiers - and the Bronze Soldier statue next to it.
The Baltic state's ethnic Russians - roughly one-third of the population - see the memorial as a tribute to Red Army soldiers who died fighting Nazi Germany and have vowed to protect it. Many ethnic Estonians, however, say the memorial is a bitter reminder of five decades of Soviet occupation.
The dispute over the monument has aggravated tensions between Estonia and Russia, which has repeatedly called on its small neighbor to halt the plans to move the grave.
"We express deep anxiety in connection with the plans of the Estonian government for transferring the buried soldiers of various nationalities who gave their lives for the liberation of Europe from fascism and for tearing down the Soldier-Liberator Memorial in Tallinn," Russia's Foreign Ministry said in a statement Thursday.
Anticipating unrest, Estonia's border guards this week stepped up security checks on the frontier with Russia and Tallinn's police force was beefed up with reinforcements from across the country.
Seven signs were posted Thursday around the site saying that archaeological work was in progress and calling for calm. About 40 police officers kept watch at the site, with dozens more waiting nearby. Police spokesman Harrys Puusepp said the situation was under control.
The government has said it wants to identify the remains in the war grave and then relocate the entire monument to a yet-undecided location. On Wednesday Prime Minister Andrus Ansip said the excavations would last up to two weeks.