"The rebel delegation is suspending the meetings because of the violent air strikes on civilians. The suspension will continue until shelling stops across all Syria," a rebel source in Astana told AFP.
Putin also discussed Syria with US President Donald Trump in a phone call on Tuesday.
Trump had previously mooted the idea of safe zones and the White House said his call with Putin included "discussion of safe, or de-escalation, zones...to achieve lasting peace for humanitarian and many other reasons."
It was the first time the two leaders spoke since Trump infuriated the Kremlin by launching a missile strike against the forces of Russia's ally Bashar al-Assad over an alleged chemical attack last month.