"The recent Russian military attacks that go beyond Daesh (Islamic State) and other UN-designated terrorist groups, as well as on the moderate opposition, are of deep concern and must cease immediately," the EU's 28 foreign ministers said in a statement.
The ministers, meeting in Luxembourg for talks dominated by the Syrian crisis, said Russia's military action only made the problem worse and weakened efforts to reach a peaceful solution.
"This military escalation risks prolonging the conflict, undermining a political process, aggravating the humanitarian situation and increasing radicalisation," they said.
The statement comes ahead of a summit of EU leaders on Thursday where Syria will also be high on the agenda.
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Ministers also said that as the crisis deepened, it became imperative to end a conflict which has claimed some 250,000 lives and driven some 12 million people - half the population - to flee their homes.
They said this required "a peaceful and inclusive transition" but it was not clear if Assad would have any role in it, perhaps reflecting sharp divisions over his immediate future.
"There cannot be a lasting peace in Syria under the present leadership," it added.
Russian President Vladimir Putin said today that Russia's military actions in Syria were meant to "stabilise the legitimate authorities and create conditions for finding a political compromise.