Russian envoy to the UN Vitaly Churkin said the move was regrettable, but that it demonstrated the gravity of the situation in the war-ravaged nation.
Mortar fire damaged the hotel building and some cars in the parking lot, including one UN vehicle.
Around 100 international and 800 domestic employees work for a variety of UN agencies and programs in the Syrian capital, Damascus.
While foreign employees are being pulled out of the country to locations including Beirut and Cairo, national staff have been instructed to work from home, UN spokesman Martin Nesirky said.
Nesirky said the organisation "remains active and committed to helping the Syrian sides in their search for a political solution".
He also said the UN would maintain enough capacity to run critical humanitarian projects and provide for people in need.
"This is a priority for the UN," Nesirky said.
About 70,000 people have died in Syria since the start of the uprising against President Bashar al-Assad in March 2011, according to UN figures.
--IANS (Posted on 26-03-2013)