"This directly harms the prospects of convening an international conference," Deputy Foreign Minister Sergei Ryabkov was quoted as saying by the ITAR-TASS news agency.
In the face of attempts by several countries to find a political solution, the European Union, pushed by Britain and France, agreed to lift its embargo on arming militants.
The bloc kept the ban over the Syrian government which has been fighting a massive Western-backed insurgency for more than two years.
Ryabkov said the 27-nation bloc is setting "double standards" by lifting the embargo against the opposition but not the Syrian army.
"We are disappointed that decisions are being reached that not only fail to promote a political solution... but which contradict the policies conducted by the European Union itself,” he said.
Western countries have already been supplying insurgents with what they call “non-lethal” equipment but the new decision marks a turning point in EU's support of the militants.
Extremist groups have swelled the ranks of insurgents in Syria and EU’s decision to arm them will lead to further insecurity which may come to haunt the West on their own doorsteps.