The order was issued a day after Russian President Vladimir Putin met his US counterpart Barack Obama on the sidelines of the 70th session of the UN General Assembly in New York.
"Carter directed his staff to open lines of communication with Russia on deconfliction," Pentagon press secretary Peter Cook told reporters at a press briefing.
He added that the US Defense Secretary is seeking to "avoid conflict in the air" between the two countries' forces.
Cook also said that the main goal of the communication channel, which was agreed upon on Monday by Putin and Obama, is to prevent US and Russian warplanes from colliding.
"The purpose of these deconfliction discussions will be to ensure that ongoing coalition air operations are not interrupted by any future Russian military activity, to ensure the safety of coalition air crews and to avoid misjudgment and miscalculation," Cook said.
He did not exclude that the communications channel may be a potential mechanism for Washington's full-fledged cooperation with the Russian military in fighting Islamic State militants.
Russia’s activities in Syria currently include supplying weapons to the Syrian government, training personnel and providing humanitarian aid to the Syrian people.
Speaking at a General Assembly session, President Putin emphasized that the Russian military's participation in a ground operation in Syria is out of question.
He said that during their meeting on the sidelines of the UN General Assembly, the two men agreed that interaction between the Russian and American military officials should continue over the crisis in Syria.
At the same time, Earnest added that the two "fundamentally disagreed" on the role of President Bashar al-Assad in Syria.
Moscow sees Assad as the legitimate head of state, while the West does not recognize the Syrian President, who US Secretary of State John Kerry said must leave as part of an "orderly transition."