Twelve inspectors led by Ake Sellstrom were seen earlier loading their luggage leaving the Four Seasons hotel in central Damascus, journalists at the scene said.
"I can confirm that the UN team has left Damascus," Khaled al Masri said. He did not reveal their destination but witnesses said the convoy headed toward the Lebanese border.
The UN team was tasked with determining whether chemical weapons had been used in Khan al-Asaal, in the northern province of Aleppo, and two other sites.