Amid a recent push from Germany, France, Italy and Spain to develop a common defense policy, von der Leyen said the EU was in need of updating its existing military resources.
"We have seen an enormous modernization drive by NATO over the past three years because of the Kremlin's behavior," she told a security conference hosted by the German Christian Democrat party.
"That was correct and important, but I believe that we must invest at the least same energy into a modernization of the European security and defense union," she added.
Russia has rejected charges of aggression in Europe, arguing that the build-up of NATO resources in eastern Europe and Baltic states had led to an increase in tension across the continent.
Impact on NATO
The idea of a joint EU military policy or greater defense cooperation was long considered an unrealistic prospect, with the UK among those member states staunchly against such proposals.
However following Britain's decision to leave the EU, officials have jumped at the opportunity to re-shape the bloc's defense policy, despite concerns from Washington that it might undermine NATO's presence in the region.
27 EU nations wanted to increase cooperation on Defence issues. This was vetoed by UK. If we are leaving, that cannot be right.#Brexit— Ron Delnevo (@RonCashman) October 21, 2016
Von der Leyen was keen to try and ease fears about the impacts such an approach would have on NATO, saying an EU modernization should take place "knowing that one cannot build up competition between the two bodies, but that they should work in a complementary fashion."
She pointed to the EU's role in trying to stem the flow of migrants and refugees across the Mediterranean as an example of how the bloc could benefit from greater military resources and cooperation.
"I see a big mission for the European Union, which must work for a solution together with the African countries," von der Leyen said. "But to do that, it must better organize and bundle the many instruments it has in the civilian and military realms, actually implement them, and offer a joint European response."
Push for Greater EU Cooperation
The comments come as some EU countries argue they should be able to respond more independently to certain crises and issues without relying on the US for support.
Proposals have included spending more on EU military missions, jointly developing defense resources and deepening cooperation.
EU defense ministers are expected to present a more detailed strategy at the upcoming December summit in Brussels.