Speaking at the Pentagon, Gates said all military-to-military activities with Moscow will be examined, and changes made, depending on Russian actions in the days ahead.
"Russia's behavior over the past week has called into question the entire premise of that dialogue and has profound implications for our security relationship going forward, both bilaterally and with NATO," he said. "If Russia does not step back from its aggressive posture and actions in Georgia, the U.S.-Russian relationship could be adversely affected for years to come."
Meanwhile, U.S. Secretary of State Condoleezza Rice has held talks in France to discuss the uneasy cease-fire that halted fighting between Russia and Georgia, where she will travel next for talks with the Georgian president.
The French-brokered cease-fire calls for Georgian and Russian forces to withdraw to the positions they held before fighting broke out a little over a week ago.
Rice's arrival in France was accompanied by reports that Russian troops remained active within Georgia in what Moscow said was part of a peacekeeping operation.
Russian troop numbers in central Georgian city of Gori had increased, according to the Georgian Foreign Ministry, and an RFE/RL correspondent reported hearing an explosion on a mountain near Gori.
Standing beside French President Nicolas Sarkozy, Rice said there must be no question about the territorial integrity of Georgia.
"The Russian president has said that their military operations have halted. We would hope that he will be true to his word and that those operations will halt," Rice said. "And we will work very hard to see if we can bring an end to this crisis. It is long overdue, too many innocent people have died."
In western Georgia, there were reports that Russian forces had entered the Black Sea port town of Poti, a key oil terminal.
The deputy head of the Russian armed forces' General Staff, Colonel General Anatoly Nogovitsyn, said at a Moscow press conference that Russian peacekeepers were carrying out intelligence operations in Poti.
Russian commanders have said their purpose now is to demilitarize conflict areas and assure security for residents following looting.
But late Thursday, Georgian President Mikheil Saakashvili told foreign reporters that a column of more than 100 Russian tanks and other vehicles was moving from western Georgia toward the country's second-largest city, Kutaisi, nearer the center of the country.
"I appeal for help -- for many people it's too late -- but I appeal [for] the help of every civilized person in the world to stop this uncivilized, barbarian, inhuman, treacherous, absolutely outrageous behavior, and to save innocent lives," he said.
RFE/RL Georgian Service correspondent Koba Liklikadze, reporting from Gori, says he witnessed heavily armed gunmen in a car with North Ossetian number plates stealing two cars belonging to Georgia's independent Imedi television and an unidentified U.S. organization. The incident took place, Liklikadze reports, directly in front of Russian soldiers in armored vehicles and tanks.
Earlier today, Russian Foreign Minister Sergei Lavrov earlier today dismissed reports that Russian forces had entered Gori and Senaki, a strategically important city on the direct rail link from Tbilisi to Poti.
"Our troops are outside the towns of Gori and Senaki. They did not enter those towns," Lavrov said. "They moved to those areas only because Georgians troops took positions there to fire on South Ossetia."
The developments unfolded as the first planeload of U.S. aid arrived in Tbilisi, signaling the start of what Washington says will be a steady stream of humanitarian aid into the country following days of intense fighting.
Nogovitsyn expressed concern at the type of cargos being flown in.
"Why not lift the curtain on what is being delivered [by U.S. airplanes to Georgia]?" Nogovitsyn said. "Although [Georgian President Mikheil] Saakashvili asked the [international] community for humanitarian aid, quite understandably, what is going on there? We, Russians, are deeply concerned about it."
The military airlift is to be complemented by U.S. naval ships delivering aid to Georgian ports in the days to come.
On the eve of her trip to France and Georgia, Rice made clear Washington's support for Georgia.
"The United States has made very clear that it is standing by the democratically elected government of Georgia," Rice said. "This is a small neighbor of Russia. It is a country that has made considerable progress in terms of its economy. It is still trying to secure its democratic institutions, and we've worked with Georgia on that. But if anyone had any doubts about our support for Georgia, you only have to look at the fact that it's a Millennium Challenge country, which is one of the most important designations that the United States can make, that we believe in the future of that country."
U.S. and EU officials have throughout the week called for respect for Georgia's territorial integrity, but Russia has been calling for Georgia's separatist regions of Abkhazia and South Ossetia to be allowed to determine their own futures.
Meeting In Moscow
Russian President Dmitry Medvedev spoke to reporters after meeting in Moscow with the leaders of the breakaway provinces, South Ossetia's Eduard Kokoity and Abkhazia's Sergei Bagapsh.
"We will support any decision that the people of South Ossetia and Abkhazia will make in accordance with the UN Charter, the 1966 international conventions, and the Helsinki Act on Security and Cooperation in Europe," Medvedev said. "We will not only support these decisions but will guarantee them both in the Caucasus and throughout the world."
Kokoity said at the press conference that "we will achieve independence" in accordance with international law.
Bagapsh, standing alongside his counterpart, said, "As for our independence, as for our movement toward this goal, no other force will stop us. We have set this goal and we will move toward this goal together. As for the ways [to achieve this goal], we will find them."
Ordinary Georgians are still reeling from the shock of the brief conflict, which began over the separatist region of South Ossetia but escalated into a Russian push into the Georgian heartland and fighting in another separatist region, Abkhazia.
"This is a nightmare, some kind of a bad dream from which one has to wake up," said Keren Esebua, a resident of the western Georgian town of Zugdidi, which also was occupied by Russian forces.
"There is immense aggression directed against absolutely innocent people. We are living under occupation," Esebua told RFE/RL's Georgian Service. "I am from Sukhumi. First [Russia] kicked me out from my home there [in the early 1990's]. Now they are also expelling us from our land. Georgia has been through the same thing twice – and no one knows for what."
'The President Has Asked Us'
Georgians from other parts of the country have rushed to help those who were caught up in the fighting.
"I brought food -- some milk, cheese and eggs. I'll leave it all here, so that it's distributed among the displaced," said Jondi Kalandadze as he brought food to refugees who had gathered at a registration center in Tbilisi. "The president has asked us [to help these people], as well as the prime minister. I'm a Georgian man. I have a little farm. Why else do I need any of it if I don't help my fellow Georgians?"
The United Nations estimates that more than 100,000 people have been displaced in South Ossetia and in Georgia proper due to the conflict. The estimate is based on numbers supplied by the Russian and Georgian governments and has yet to be independently confirmed by international agencies.