Syrian ambassador to Iraq Nawaf Fares, who announced his defection to the opposition, is now in Qatar, Foreign Minister Hoshyar Zebari said on Thursday.
"The Iraqi ambassador left the country and is now in Qatar," Zebari said in remarks broadcast by Al-Iraqiya television.
Fares defected on Wednesday and urged the army to turn its guns on the regime, becoming the first ambassador to abandon President Bashar al-Assad.
"I announce my defection from my post as representative of the Syrian Arab Republic in Iraq and my withdrawal from the ranks of the (ruling) Baath party," Fares said in a message aired on Al-Jazeera satellite channel.
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"I call on all free and worthy people in Syria, particularly in the military, to immediately join the ranks of the revolution," he said. "Turn your cannons and your tanks towards the criminals in the regime who are killing the people."
His remarks were denounced in Damascus.
The foreign ministry issued a statement saying that Fares has been "discharged" and "needs to be legally prosecuted and subjected to disciplinary action" due to his remarks which contradict his duty.
Qatar has been at the forefront of calls to arm the opposition in Syria against the regime of President Bashar al-Assad and took the lead to mobilise the international community against against Damascus over its 16-month crackdown on dissent.
Fares, who hails from a prominent Sunni tribe from eastern Syria, had been the Damascus envoy to Iraq since September 2008 and was a prominent member of the ruling Baath party.