In response, the Kremlin said it was "disappointed by the decision," RIA Novosti reported.
The White House decision followed Russia's action granting temporary asylum to Edward Snowden, a former employee of the National Security Agency wanted by the United States for leaking national secrets.
In a statement, the White House said it had called off talks with Putin because "we have reached the conclusion that there is not enough recent progress in our bilateral agenda."
The talks would have touched on missile defense and arms control, trade, global security and human rights, the statement said.
The White House admitted a factor in canceling the talks was Russia's "disappointing" decision to grant asylum to Snowden.
Yury Ushakov, Putin's top foreign policy aide, said it was "clear" Snowden's asylum had prompted cancellation of the talks, but said Snowden's situation "was not created by us."
Ushakov said the Kremlin remained ready to collaborate with the United States on "key issues of the bilateral and international agenda."
In an interview with late-night host Jay Leno Tuesday, Obama said Russia's foot dragging in the Snowden controversy was "reflective of some underlying challenges that we've had with Russia lately."
He accused Russian officials of returning to a "cold war mentality."
Obama has said he still plans to attend a September Group of 20 summit in St. Petersburg, Russia.
In another statement Wednesday, the White House said Obama would make a two-day visit to Sweden before the start of the summit.
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