Speaking at a joint news conference after a summit with European Union leaders, Putin said Russia was disappointed by an EU decision not to extend an embargo on member states arming militant forces fighting the Syrian government.
A crisis that has already cost thousands of lives has threatened in recent weeks to turn even more dire with a controversial decision by the European Union to free shipments of arms to the militant and terrorists groups in Syria by not extending its arms embargo on the armed groups.
Putin referred to the war crimes committed by anti-government side in Syria, saying that widely circulated footage of an al-Nusra Front terrorist eating the body parts of a slain Syrian soldier had threatened to derail attempts for finding a solution to the crisis.
"I hope that such participants of the negotiations do not appear" at the proposed Geneva talks, Putin said.
"Otherwise, it will be hard for me to ensure the safety of the Russian participants. It would be hard to work with such people."
The Syrian crisis and the European Union's decision, on May 28, to lift its arms embargo on militants dominated the regular Russia-EU summit.
Western countries have already been supplying insurgents with what they call “non-lethal” equipment but the new decision marked 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 is expected by many to lead to further insecurity which may come to haunt the West on their own doorsteps.