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An occasional touch-and-go alliance between the United States and Russia since the end of the Cold War appears to be moving toward a rough patch as Russian President Vladimir Putin (search) makes moves to turn the country in on itself.

The two nations' relationship apparently had been strengthened by the cordiality between President Bush (search) and Putin. But recent events, including Russia's decision to sell off the assets of its nation's oil firm and disagreements over the outcome of the invalidated Ukraine election, have put a strain on the alliance.

Putin has also been accused of rolling back civil reforms established in the 1990s and eliminating press freedoms and political pluralism.

For his part, Putin was edgy and defensive on Wednesday when asked at his end-of-year press conference about his views on democracy in Russia, the Ukraine and elsewhere. Putin has personally campaigned for pro-Moscow Ukrainian Foreign Minister Viktor Yanukovych, who won last month's nullified election after the country's Supreme Court validated charges of massive voter fraud. The new election was scheduled for Sunday.

"I repeat, we are not going to annex anything," Putin told reporters of his intentions toward Ukraine. Instead, Russia's second democratically elected leader has repeatedly accused the West of interfering in the Ukranian election, and has lashed out at the United States indirectly, though he said Thursday that he does not think that U.S. policy is to marginalize or isolate the Russian Federation. He added that he considers Bush a decent and consistent man whom he trusts.

But Russia did test-launch this week an SS-18 missile (search), also known as the Satan rocket, which is able to carry multiple warheads, and Putin said controlling weapons and non-proliferation form the basis of the U.S.-Russian relationship.

Back in the United States, some observers have said that the contested Ukrainian election has opened a door for the administration to be more vocal about its differences with Russia.

"This story is tremendously important, perhaps the greatest story in the world right now, largely because it is about the space of freedom," Sen. Richard Lugar, R-Ind., an observer of the disputed election, told FOX News following the first vote. Lugar said the election was marred by "wholesale fraud and abuse."

Lugar's comments were seemingly backed by outgoing Secretary of State Colin Powell, who refused to accept the election results and added that Russia may be defying an international treaty by failing to acquire host country agreement to the stationing of its forces in Moldova and Georgia, members of the Organization for Security and Cooperation in Europe (search).

He added at a meeting of the 55-nation OSCE in early December that the United States remains "concerned about developments in Russia, most notably those affecting freedom of the press and the rule of law."

Trying to Maintain the Peace

Others urge Washington to tread carefully with its sensitive ally after Bush's election pledge to be more aggressive in securing loose nuclear materials.

When Bush first met Putin, he declared he "was able to get a sense of his soul." On Monday, he repeated his commitment to his ally.

"Vladimir Putin and I have got a good personal relationship, starting with our meeting in Slovenia," Bush said during his year-end news conference. "I intend to keep it that way."

Despite the close personal affinity, many Russia observers in the United States say the two nations have always had a somewhat tense relationship, and learning how to communicate differences has been an "enduring problem" for the two since the end of the Cold War.

"President Bush can speak directly [to Putin], but only privately, on everything from the apparent crackdown on independent media to the spontaneous reorganization of the country's political life," Coit Blacker, director of the Stanford Institute of International Studies (search), told FOXNews.com.

Blacker added that differences have been discussed largely behind the scenes, especially since the Sept. 11, 2001, terror attacks, when Putin was the first world leader to phone President Bush and express his support in fighting terrorism.

"The Bush administration has been careful about criticizing Russia's internal politics — they don't want to offend Putin," said Olga Oliker of the RAND Corporation (search) think tank. "The U.S. fears if it's too critical, it'll be impossible to move forward on areas of cooperation."

But Kyle Parker, a Russia analyst at the American Foreign Policy Council (search), said the rising volume of reports on nuclear proliferation, the conflict in Chechnya, the bankruptcy of Russian oil giant Yukos and the Ukraine elections will make it harder to operate strictly behind closed doors.

"It's increasingly difficult to ignore the authoritarian drift in Russia," Parker told FOXNews.com. "Americans who didn’t necessarily follow U.S.-Russian relations might be scratching their heads and wondering why we're so buddy-buddy with Putin."

A New Approach in the Works?

A State Department official told FOXNews.com that the department was "taking stock of achievements" and "identifying priorities for our bilateral agenda" with Russia. This comes as the diplomatic agency transitions from Powell to the next secretary of state, most likely to be current National Security Adviser Condoleezza Rice (search), who is expected to win confirmation in the Senate following hearings next month.

The official stressed the review is part of the normal process that occurs during a leadership transition and declined to say whether a more critical attitude is developing in the department toward Russia, as has been speculated in recent media reports.

Rice, a former provost of Stanford University, is an expert on the former Soviet Union and served as the top security adviser on that nation to President George H.W. Bush. After the Sept. 11 attacks, the administration's critics were quick to pounce on Rice's Cold War background, charging that she did not have the goods to take on Islamic extremism.

Now, however, her background may fit the occasion. Though as national security adviser, she has not openly criticized Moscow, she previously accused the Clinton administration of not being more stern with then President Boris Yeltsin (search ), referring to its engagement with Moscow as "happy talk."

"My understanding is she does see Russia through those Cold War lenses," said Andrew Jack, Moscow bureau chief at The Financial Times and author of "Inside Putin's Russia: Can There Be Reform Without Democracy?"

"That means there's an instinctively more confrontational approach, an older approach to looking at relations," Jack told FOXNews.com.

But Rice remains a close friend and valued adviser to the president and is known for her loyalty to the administration and for running a tight-lipped ship. If she plans to depart from the company line at all, said Blacker, a friend and former Stanford colleague, she'll do so behind closed doors and not through press leaks.

"If she disagrees [with the administration] she won't be the one doing the leaking," Blacker told FOXNews.com. "In their private counsel, she will be capable of articulating her point of view or argument.

"One thing I expect is that Condi Rice is going to pay a lot of attention to the important bilateral relationships this county has, and that includes Russia," said Blacker, adding, "This administration has been more gentle with Putin than some of us would prefer."

Forcefulness will be required as Russia's security problems also stand to threaten America, warns John Pike of Globalsecurity.org. Pike said believes he Putin's tendency to view the War on Terror through a Cold War lens has led him to frame his country's security in terms of geography and military might, leaving a wealth of nuclear materials vulnerable.

"Putin's definition of security is how many kilometers stand between him and NATO," Pike told FOXNews.com.

RAND's Olicker said more needs to be done to secure Russia's nuclear materials. She cited a Nuclear Threat Initiative report that found the amount of "loose nukes" material secured since the Sept. 11 attacks has actually dropped.

Olicker also argued that political setbacks in Russia, such as a Putin-endorsed end to popular elections for local leaders, leave the country's security forces weak and disorganized. Russian security forces were also blamed for botching the rescue operation of 1,000 people taken hostage on the first day of school in the Russian town of Beslan in September. Chechen and foreign Muslim fighters killed hundreds of hostages, mostly children.

Jack said he's not sure that the administration will say much about Russia's affairs, particularly since the Iraq war remains a divisive point in relations.

"When you look at the foreign policy, the administration under Bush has shifted the goalposts a lot," he said. "I would say there's a pragmatic alliance between Bush and Putin about not interfering too far in foreign affairs."

But Parker said Washington should not be afraid to take off the kid gloves.

"Russians respect candor and power — they find weakness provocative and not to be respected. Russians had great respect for Reagan. They liked" his directness, Parker said.

FOX News' Dana Lewis contributed to this report.