"The militarization of the Turkish-Syrian border would be an alarming signal," said ministry spokesman Alexander Lukashevich. "It would do nothing to foster stability in the region."
"Our advice to our Turkish colleagues is to use their influence on the Syrian opposition to draw them closer to dialogue, instead of flexing their muscles and taking the situation down a dangerous path," he added.
NATO Secretary General Anders Fogh Rasmussen said Wednesday that Turkey's request to deploy the missiles would be considered soon. Ankara says the missile system is necessary to protect its border with conflict-torn Syria.
US Patriot surface-to-air missiles were last deployed to Turkey in 1991 and 2003, during the two Gulf Wars.
Turkey has opened fire several times in recent weeks across its border with Syria in retaliation for Syrian shelling, which killed five Turkish civilians in October. It has also provided shelter to refugees fleeing the violence in Syria and has been one of President Bashar al-Assad’s harshest critics during the almost 17-month revolt against his rule.
Tensions between Turkey and Syria flared dangerously this summer after Damascus shot down a Turkish fighter that had violated its airspace. Turkey threatened retaliation if there was any repeat of the incident, although it admitted the plane had mistakenly strayed slightly into Syria.
Lukashevich also denied Russian media reports that Foreign Minister Sergei Lavrov was planning to meet on November 26 with the Syrian opposition.
The Syrian conflict has claimed tens of thousands of lives since the start of an uprising against Assad in March 2011, according to various Syrian opposition groups.
Russia - along with China - has drawn heavy Western criticism for its refusal to sanction UN sanctions against Assad's regime, Moscow sole remaining ally in the Arab world. Moscow said the proposed UN resolutions betrayed a pro-rebel bias and would do nothing to bring peace.
Putin vowed earlier this year not to allow a repeat of the "Libya scenario,” which saw the ouster and murder of long-time Libyan dictator Muammar Gaddafi after a NATO military campaign.
But Moscow has denied it is supporting Assad in the conflict and says it will respect the will of the "Syrian people."