Speaking at the 45th Munich Conference on Security Policy, Jaap de Hoop Scheffer identified two partnerships that need fundamentally strengthening - the second being between Europe and the United States.
He said that the NATO-Russia Council had great potential but warned there was a long way to go, expressing doubts about Russian President Dmitry Medvedev's proposals for a new European security structure in the wake of Russia's recognition of and cooperation with the separatist Georgian republics of South Ossetia and Abkhazia.
"I cannot see how we can have such a serious discussion of such a new architecture, in which President Medvedev himself says territorial integrity is a primary element, when Russia is building bases inside Georgia, a country that doesn't want those bases," Scheffer said.
"That cannot be ignored and it cannot be the foundation of a new European security architecture," he said.
On Europe's relations with the United States, the NATO head said coming together must be a "two-way street" and singled out Afghanistan as a potential litmus test.
"I'm frankly concerned when I hear the United States is planning a major commitment for Afghanistan but other allies are already ruling out doing more," he said. "That is not good for the political balance."
"The Obama administration has already done a lot of what Europeans have asked for including announcing the closure of Guantanamo and a serious focus on climate change," he said. "When the United States asks for a serious partner, it does not just want advice, it wants and deserves someone to share the heavy lifting."
U.S. Vice President Joe Biden is due to speak at the conference later on Saturday.
