At a recent meeting, the two men discussed Russia-NATO cooperation, particularly in the fields of countering terrorism, weapons of mass destruction proliferation and the settling regional conflicts.
Putin afterwards praised what he called Russia's "successfully developing" relations with NATO.
"We have left old Cold War threat perceptions behind us, because our real threats are clear: terrorism, the proliferation of chemical, biological and nuclear weapons and materials, failed states and regional conflicts, trafficking in arms, humans and narcotics," Scheffer told reporters.
He told Putin that there were no plans to open military bases on Russia's doorsteps and that the U.S. tactical nuclear weapons deployed in the bloc were of "political" significance only.
In an earlier interview with the Interfax news agency, the NATO chief had stated "there is simply no NATO plan to shift a constant military presence toward Russian borders."
He also said NATO and Russia were committed to exercising restraint in deploying conventional forces.
The limited presence of NATO and American forces in Central Asia, deployed in the wake of the 9/11 terrorist attacks, should not be perceived as "threats to Russian interests," Scheffer said.
The two men also discussed the possibility of cooperating in efforts to curb the narcotics trade in Afghanistan and Central Asia, which Scheffer called "a very destabilizing factor."
After he met with the NATO chief, Foreign Minister Sergei Lavrov voiced concern about anti-Russian terrorists being training on Afghanistan soil by members of the Taliban and other Islamists.
"We are ready to work on this with NATO in the framework of our joint plan for fighting against international terrorism," he said.
Lavrov also urged NATO to ratify an amended version of the Conventional Armed Forces in Europe Treaty, an agreement signed in 1990 that limits the deployment of non-nuclear weapons.
The agreement was modified in 1999 to reflect geo-political changes after the collapse of the Soviet Union. But NATO has refused to ratify the amended version of the treaty, saying Russia breached it by failing to pull out troops from the former Soviet republics of Georgia and Moldova.
Fearful of possible NATO military bases on its doorsteps, Moscow wants newcomers in the European Union, including the Baltic states of Estonia, Latvia and Lithuania, to commit to the treaty.
Lavrov complained that linking the treaty with its Soviet-era bases was not valid, while Scheffer reaffirmed it.
Despite the disagreement, Russian officials sounded upbeat.
"We are working actively to build a real partnership with NATO," said Lavrov, adding that cooperation was based on common interest in fighting terrorism, drug trafficking and curbing proliferation.
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