Theodora Bakoyianni said the atmosphere was "not very pleasant" as ministers discussed Russian President Vladimir Putin's state of the nation address.
Later, Greek Foreign Ministry spokesman Yorgos Kumutsakos explained that Greece was not talking about an intention to host any missile defenses.
"We have long highlighted the importance of joint agreed efforts to address common challenges and threats. Missile defense is not an exception. This issue requires a common discussion with NATO and Russia," Kumutsakos said.
In his address, the Russian leader called for suspending Russia's participation in the Treaty on Conventional Forces in Europe, citing Western non-compliance and U.S. plans to deploy part of its missile shield in Poland and the Czech Republic on a bilateral basis.