Speaking in Madrid at the start of a five-day trip to Europe, Carter told Spanish military officials that by carrying out bombing in Syria, Russia had only worsened the four-year conflict.
Russia last week started air strikes in Syria, claiming it was hitting Islamic State jihadists. But the Pentagon says Russian jets have targeted other rebel groups in order to support the regime of President Bashar al-Assad.
"Russia has escalated the civil war, putting further at risk the very political resolution and preservation of Syria's structure of future governance it says that it wants," Carter said.
Carter's trip is aimed at acknowledging allies in the 60-plus member US-led coalition that is carrying out daily drone and plane strikes against IS jihadists in Iraq and Syria.
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Turkey on Monday said its F-16 jets had at the weekend intercepted a Russian fighter plane which violated Turkish air space near the Syrian border, forcing the aircraft to turn back.
It demanded that "any such violation not be repeated", otherwise Russia "will be responsible for any undesired incident that may occur."
The tour comes at a fraught time for Carter, who started in the Pentagon's top job in February and who faces pressure at home over Syria and a simmering scandal involving military officials allegedly cherry-picking intelligence.
Adding to Carter's woes is the fallout from a suspected US strike that hit a Doctors Without Borders (MSF) hospital in the Afghan city of Kunduz on Saturday, killing 22 people, some of whom burned to death in their beds.
The US military has not confirmed that it was responsible for the devastation, but has said it deployed an AC-130 support plane to help US special operations forces on the ground near the hospital.