Although the Russian leader called the talks generally positive, he said key differences remained on the issue of strategic arms.
At a news conference after the talks in Sochi, Putin, who will leave office in one month, said: "Our position on the U.S. [missile defense shield] plan remains unchanged."
Russia views a planned U.S. missile base in Poland and a radar in the Czech Republic as a direct threat to its security and has rejected Washington's assurances that they were designed as protection against Iran and other Middle East states.
"As for strategic offensive armaments, some disagreements remain in our basic approaches," the Russian leader said.
Bush also met with Russian president-elect Dmitry Medvedev, who is set to take over in the Kremlin on May 7 when Putin steps down.
