Rice arrived from Beijing at midday for a flurry of meetings with Putin, Foreign Minister Sergei Lavrov and Defence Minister Sergei Ivanov that were to focus primarily on implementing UN Security Council resolution 1718 imposing sanctions on North Korea over its recent nuclear test.
But she found time to meet at her request with editors of Novaya Gazeta, the independent newspaper of slain investigative journalist Anna Politkovskaya, and also questioned the Russian leaders over human rights issues.
Rice requested the encounter, which took place in a Moscow hotel, a State Department official said.
Politkovskaya's son, Ilya Politkovsky, 28, was also present.
The journalist, a prominent Kremlin critic who investigated corruption and human rights abuses, was gunned down this month outside her Moscow apartment in what police said was a contract killing.
No arrests have been made in the case, the 13th apparently deliberate killing of a journalist since Putin came to power in 2000.
Independent media have dwindled significantly under Putin's rule, with virtually all television networks now under state control and many radios and newspapers held by interests close to the Kremlin, US officials said.
Two days after Politkovskaya's October 7 murder, Rice warned the Russian government "that everybody is watching, that an investigation of this event is absolutely necessary."
In an emotional encounter, Rice, a Russia scholar and expert in the history of the former Soviet Union, briefly addressed the group in Russian before making a few remarks in English on the purpose of her one-day Moscow visit.
A senior State Department official said Rice wanted to hold the meeting "as part condolences... and part support for what is left of a free media in Russia."
He denied the meeting was intended as a slight to Putin.
"We certainly didn't plan it as a poke in the eye, but the right thing to do," he said.
In addition to concerns about press freedom under Putin, Rice said she and her aides would ask about a new law requiring foreign non-governmental organisations (NGOs) to register with authorities.
The NGOs, including Amnesty International and Human Rights Watch, have complained that the law is a bid by Putin to monitor and restrict their work, which often involves investigating alleged human rights abuses in the country.
A deadline for registration passed on Thursday and a number of NGOs that did not submit their documents in time were forced temporarily to suspend their operations, though Russian officials said most did comply on time and promptly received new registration.
The State Department's point man for Europe, Dan Fried, discussed the issue Saturday with Russia's Human Rights ombudsman, Vladimir Lukin, a senior official said.
While the Americans welcomed the fact that some major US NGOs had received their registration, there were still concerns the law could be misused in future, the official said.
"I can't say with confidence that the Russians will not abuse this law," he said.
Rice and her delegation also raised the flare-up in tensions between Russia and the pro-US government of the former Soviet republic of Georgia and reports of harassment of Georgians living in Russia.
Relations between the two states soured dramatically after Georgia arrested four Russian military officers accused of spying last month.
The four were quickly released, but the two governments remain locked in confrontation over two breakaway Georgian regions, Abkhazia and South Ossetia, which have received support from Moscow.
Georgia has threatened to use military force against the rogue regions, a move that could spark a conflict with Russia.
"Cooler heads need to prevail here... because that is the kind of problem that can get out of control," Rice said before meeting with the Russians.
The senior official said the two sides held constructive talks on the crisis and "the Russians acknowledged that they don't want to go over the cliff, to have some terrible blow-up with the Georgians that destabilises the South Caucasus."

Copyright AFP (Agence France-Presse), 2006