Resistance was slow to emerge. It was given much greater urgency when the prospective insurgents learned about plans for mass deportations. On June 14, 1941 the Soviet government began mass deportations, sparking armed resistance. Although the guerillas were able to engage sizeable government units and inflict substantial casualties, the violence remained below the threshold of civil war until Germany attacked the USSR on June 22.

Within a day, the Lithuanian Activist Front, which had been armed by Germany, rose against the government. In three days of fighting, the rebels – between 38,000 and 100,000 strong -- suffered about 2000 killed. By June 26, the USSR also admitted to a Latvian insurrection (which may have had 60,000 rebels); two days later, the Latvian rebels expelled government forces from Riga for a day, provoking a vicious government counterattack. Latvian resistance ended with the fall of Riga to the Germans on July 1.

Estonian resistance began with the deportations, but on a much smaller scale.
It only really escalated to full-scale rebellion on July 1 with an engagement at Kiviõli that killed 8 government troops and one of the rebels (called Forest Brethren -- Metsavennad in Estonian). From July 4-5, a rebel ambush at Kilingi-Nõmme killed several hundred government soldiers. In northern Estonia, Finland contributed to the creation of a unit mobilized from Estonians serving in Finland called “Erna,” which first engaged the government’s forces on July 31. The rebels sought some assurance from the advancing Germans that Estonian independence would be respected, but received none. As the Germans advanced into Estonia, the rebels (by now about 30,000-strong) fell back, continuing to fight government forces until the occupation of Talinn on August 28.

The Germans quickly ousted the Estonian guerillas from their “liberated areas” and planned to deport them. Thus, neither the Metsavennad nor the government were able to secure a military victory. The war would erupt again upon Soviet reoccupation of the Baltics.

While sources agree that Metsavennad losses amounted to 541 killed or missing (presumed dead), they disagree about government losses. While Misiunas and Taagepera (1993) state that government losses were “comparable,” Shtromas (1994) argues that the Metsavennad inflicted 4800 battle-deaths on the Red Army during the two months of fighting.

Sources:

Laar, Mart. 1992. War In the Woods: Estonia’s Struggle for Survival, 1944-1956. Transl. Tiina Ets. Washington, DC: Compass Press.

Misiunas, Romuald J. and Rein Taagepera. 1993. The Baltic States: Years of Dependence, 1940-1990. Expanded and Updated Ed. London: Hurst and Co.

Shtromas, Aleksandras. 1994. “The Baltic States as Soviet Republics: Tensions and Contradictions.” The Baltic States: The National Self-Determination of Estonia, Latvia, and Lithuania. Ed. Graham Smith. London: Macmillan, pp.86-120