Washington wants to place 10 interceptor missiles in Poland and a radar station in the Czech Republic at a cost of $3.5bn.
Henry Obering, the US air force lieutenant general and director of the US missile defence agency, said bases in Poland and the Czech Republic would be designed to destroy missiles being developed by Iran.
Two other bases in Alaska and California would protect the US from threats from North Korea, he said.
After meeting with Gates, Anatoly Serdyukov, the Russian defence minister said: "The strategic missile defence system is a serious destabilising factor which could have significant impact on regional and global security."
A senior administration official travelling with Gates said the defence secretary would press Putin on a deal offered to the Russians last week to share benefits of the system such as data and possibly technology.
"We outlined a series of areas where we might be able to co-operate with Russia and this involves both sharing of information and potentially of technology," a senior administration official said.
"It includes things like sharing sensor data for early warning, common research and development, testing of various components of systems."
But the Pentagon intends to move forward whatever the response, the official said.
"We're going to continue to make this effort with Russia but we're also very clear, whether Russia cooperates with us or not is really up to Russia," the official said on Sunday.
US officials cast the issue in technical, not political, terms and argue that the systems Washington wants to put in Poland and the Czech Republic cannot be used to defeat a Russian missile.
But Russians voice both technical and strategic problems with US plans.
Some Russian officials have argued the sites are so close to Russia's borders that they could harm its security. Some also say the US could eventually equip the sites with offensive weapons aimed at Russia.
"We would want to hope that Washington listens to our views and concerns, although I am not much of an optimist on this issue"
Igor Ivanov, secretary of Russia's security council
Russian officials say they support exploring a collective missile system that would protect against rogue states, but are annoyed that Washington has gone ahead unilaterally.
Igor Ivanov, secretary of Russia's security council said he held little hope the discussions would yield a quick resolution on the missile defense dispute.
"We would want to hope that Washington listens to our views and concerns, although I am not much of an optimist on this issue," he said.
Missile defence is only one sign of deteriorating relations between Washington and Moscow.
While the US has made accusations that Russia is rolling back democracy and trying to revive past imperialism, Moscow charges Washington with acting unilaterally and meddling in its domestic affairs.
Russia and the US have different approaches to Iran's nuclear programme, which the West suspects is to develop atomic weapons and Tehran says is to generate power. A Russian contractor is building Iran's Bushehr nuclear power plant.
Washington also criticises Russia for selling anti-aircraft missile systems to Iran, saying it undermines regional security.
The US defence secretary will travel to Poland and Germany to discuss missile defence after his talks in Moscow.