The talks appeared aimed at ironing out growing tension between Moscow and the Western military alliance.
Seated at a table alongside Russian officials in one of the Kremlin's ornate halls, Scheffer was quick to praise Russia's role in the international arena.
"Russia carries great responsibility in world affairs," he told Putin in televised opening comments. "Russia's active participation for the solution of many conflicts is essential."
Putin gave an equally upbeat assessment of ties between Russia and NATO, which in 2002 signed a partnership agreement outlining cooperation in areas such as counterterrorism, nonproliferation, and peacekeeping.
"We continue [NATO-Russia] cooperation in assisting NATO countries in Afghanistan, we have now joined your work in the Mediterranean Sea, our Emergency Situations Ministry is cooperating [with NATO] on emergency response planning," Putin said. "I would also like to note our political dialogue, which is maintained constantly and at the highest level."
Once the reporters were ushered out of the room, however, Putin is expected to have voiced strong concern about NATO's plans to embrace other former Soviet countries.
The Baltic States' accession to NATO in 2004 and Ukraine's intention to join the alliance have been met with alarm in Moscow.
Now the Kremlin is upset by NATO's recent decision to launch what it calls "intensified dialogue" with Georgia, whose president Mikheil Saakashvili has pledged to take his small Caucasus country into NATO in 2008.
He said Putin intended to raise this issue during talks with Scheffer.
Relations between Moscow and Tbilisi, already strained by Saakashvili's Western-oriented policy, hit a new low after Georgia's brief arrest of four Russian military officers on spying charges last month.
Moscow responded by slapping a transport blockade on Georgia and cracking down on Georgian migrants and businesses in what many describe as the worst diplomatic crisis between the two neighbors in the past decade.
Scheffer called on Russia to lift the sanctions against Georgia in comments to journalists after today's Kremlin meeting.
Yevgeny Volk, the head of the Moscow branch of the Heritage Foundation think thank, says Russia is worried at the prospect of NATO presence in a region it continues to regard as its own backyard.
"Russia does not want its political influence and its economic positions to weaken in the post-Soviet space," Volk said. "NATO membership is a springboard of sorts for membership in European economic and political structures. So for the Russian leadership, Georgia's entry into NATO is a kind of nightmare that they would like by any means to prevent."
According to the Russian Foreign Ministry's Grushko, Putin also planned to express Moscow's irritation at the NATO's refusal to ratify an amended version of the Conventional Forces in Europe (CFE) Treaty. This agreement set limits on the number of troops and armament deployed across Europe.
NATO member states say they will not ratify the new version of the treaty, which addresses changes since the Soviet collapse, until Russia withdraws all troops from the former Soviet republics of Moldova and Georgia.
Grushko said that Russia could choose to pull out of the agreement should NATO continue to drag its feet.
Georgian deportees arriving in Tbilisi on October 6 (epa)
RUSSIA DEPORTING GEORGIANS. Despite Georgia's release of four military officers accused of spying on October 2, Russia has continued its transport and postal blockade of Georgia, and has also deported hundreds of Georgians.... (more)