But Putin added that bilateral economic and political relations with Germany are very good.
"This [visit] is not a simple coincidence of circumstances," he said. "This is a confirmation of the privileged character of bilateral relations. This is a confirmation of our mutual will to firmly move toward deepening our strategic partnership between Russia and Germany -- and I have no doubt that in the coming years this course will continue."
The outgoing president made the comments today after talks with Merkel at the presidential residence in Novo-Ogaryovo, outside Moscow.
Merkel, for her part, said relations between the two countries are always a joy, but "sometimes a challenge."
The chancellor also said she thinks there will be "good cooperation" with Medvedev. But she also stressed that Germany favors "critical and open dialogue."
The German chancellor later headed to talks with Medvedev at the nearby Meiendorf Castle to become the first Western leader to meet the designated president since his landslide victory in the March 2 presidential election.
Merkel was expected to stress the importance of German-Russian relations to Medvedev and learn first hand what plans he has to modernize Russia and strengthen its democratic structures.
Merkel, who has in the past scolded Putin over human rights, has also sought to boost trade with Russia's booming economy and to mediate between Moscow, Washington, and Russia's EU partners.
On the agenda at today's talks are Iran, Kosovo, gas supplies to Europe, and boosting bilateral trade.
Germany is by far Russia's biggest single trading partner, with a record $52.8 billion in bilateral trade in 2007.
RFE/RL's Russian Service contributed to this report