Russia has called on the US to "freeze" plans to employ missile defence facilities in eastern Europe.
Condoleezza Rice failed to break down Sergei Lavrov's opposition
After high-level talks in Moscow, Foreign Minister Sergei Lavrov said Russia saw the shield as a "potential threat" and wanted to "neutralise" it.
US Secretary of State Condoleezza Rice denied any threat to Russia, saying she wanted both countries to work together.
Earlier, however, Russian President Vladimir Putin signalled he would not support American plans.
He urged Washington "not to force" a planned deployment - of a radar in the Czech Republic and interceptors in Poland - on Russia.
Mr Putin also threatened to abandon a key nuclear missile treaty which he said was outdated.
After meeting President Putin Ms Rice went into a "2+2" meeting with her counterpart, Mr Lavrov, and the two countries' defence secretaries, Robert Gates and Anatoly Serdyukov.
The atmosphere afterwards was glum, says the BBC's Richard Galpin in Moscow. It was clear the two sides had made little progress in tackling the increasing number of problems dogging their relationship.
Mr Gates said he and Ms Rice had put several new ideas to the Russians, but indicated that they had not yet been accepted.
"Our talks reflected the complex, multi-faceted relationship the US and Russia have," he said.
"We remain eager to be open and full partners with Russia in missile defence... we discussed a range of proposals we hope they will accept."
The US says it needs a missile defence system to counteract "rogue states" like Iran and North Korea.
The Kremlin has asked the US why it cannot instead use Russian-operated early warning radar in Azerbaijan.
Mr Gates said while that radar might be used, it was not capable of guiding interceptor missiles.
President Putin said at the start of the talks that it would be difficult to remain part of the Intermediate Range Nuclear Forces (INF) treaty unless it was expanded to include more countries than just the US and Russia.
The reason, he said, was that other countries were developing these kinds of weapons systems - including those close to Russia's borders.
Analysts say President Putin's threat to withdraw from the treaty is yet another diplomatic move to pressurise the Americans.
The treaty, which limits US and Russian short and medium range missiles, was signed 20 years ago and led to the elimination of almost 3,000 Russian and American missiles.
Split on Iran
Russia has also threatened to leave the Treaty on Conventional Armed Forces in Europe if it is not ratified by all Nato nations.
Russian defence analyst Alexander Goltz said this military agenda for the talks suited Mr Putin as it distracts his Western critics from the subjects of democracy and human rights.
Mr Putin does not want any Western interference into his plans for continued political involvement when he has to stand down as president next March, Mr Goltz said.
The US-Russian talks also covered the Iranian nuclear issue, after which Mr Lavrov criticised US sanctions and US hints about using military force against Iran, which he said "contradict our collective efforts" to negotiate a solution.
Ms Rice and Mr Gates were in Moscow for two days of talks, which were also expected to cover Kosovo and a nuclear weapons treaty to succeed START, which expires in 2009.
US MISSILE DEFENCE: LONG RANGE THREAT PROTECTION
US wants to build defence system against possible missile attacks
Part of defences would be in Eastern Europe - which Russia opposes
Russia suggests US should use its Gabala, Azerbaijan base instead