"Why did they do this? Nobody knows the answer to that question," Putin said.
Russia's lawmakers responded to the Magnitsky list with their own list, slapping similar sanctions on 18 Americans it called rights violators.
Putin also said he is grateful for the Obama administration's support of Russia's entry to the World Trade Organization but questioned why it still has Cold War-era legislation -- the so-called Jackson-Vanik amendment -- governing its trade relations with Russia.
The United States has waived the legislation every year since 1994, but it still violates World Trade Organization rules requiring members of the body to give one another permanent normal trade relations.
NATO's engagement in the Libya conflict also led to cooler relations, Putin said.
The session was Putin's 11th televised question-and-answer conference, according to Russian state-run broadcaster RT.