Paulo Pinheiro stopped short of directly criticising the United States or other nations arming Syrians, saying the commission does not comment on decisions by governments. But his remarks came about a week after President Barack Obama authorised sending weapons to rebels for the first time.
It marked a major policy shift for the Obama administration, and came after the White House disclosed that the US had conclusive evidence that Bashar Assad's regime had used chemical weapons against the opposition trying to overthrow him.
"We are very much worried that more arms will signify an increased presence of violations and those crimes," he said.
The UN Commission of Inquiry earlier this month in a report to the UN Human Rights Council in Geneva accused both sides of committing war crimes in Syria. About 93,000 people have been killed in Syria since the first protests began in March 2011.
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"Crimes that shock the conscience have become reality ...We emphasise that there is a devastating human cost to the availability of weapons and that there is also a political cost," Pinheiro said. "Weapons fuel the parties' illusion that they can win this war, pulling them farther into battle and away from the negotiating table."
No date for those talks has been set, but leaders at the Group of Eight who met this week in Northern Ireland all agreed talks should start soon.