The visit comes as officials say Washington's relationship with the Western military bloc is at its strongest in decades.
"This month the US and NATO have achieved their highest operational tempo of training and exercises since Cold War," a US defense official said Friday.
The US official said Carter's visit is a chance to "acknowledge" how NATO member nations have responded to Russia's actions in the region, and also to discuss "what we need to continue doing."
While in Tallinn, Carter will meet with defense ministers from Baltic States Estonia, Latvia and Lithuania, the Pentagon said, two of which border Russia.
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All three countries have issued calls for the permanent presence of NATO troops in their territory.
But NATO states have been reluctant to grant he request, as deploying troops could undermine its Founding Act, signed with post-Communist Russia, to build a "lasting and inclusive peace."
The Pentagon official said the material would be used to train US troops in the region, downplaying Kremlin accusations that NATO was threatening its borders.
"The material is currently allocated to Germany. The question we asked ourselves last year, over the period of increased exercises in Eastern Europe, is where is the optimum place to store the material to be efficient," the US official said.