Staff attached to the Irish Relief organisation GOAL and Concern have been moved to a safe house in the East Timorese capital, Dili.
A state of emergency has been declared there after riots.
Police shot dead at least two students during a demonstration, sparking the rioting and looting.
The Prime Minister's home in Dili has been burned down in the worst violence since the country won independence from Indonesia.
GOAL's East Timorese Director, Anne McGuire, who is in Dili, witnessed some of the trouble before being taken to a safe house.
She said: "There were just thousands of people running into our office trying to get away from all the rioting.
"They were throwing petrol bombs. In the restaurant beside me, they are throwing rocks, they completely looted the place, all the windows are smashed.
"They came for the GOAL offices then and they threw rocks at our offices but our security officers then went out and said this is not international, our organisation was not UN, and thankfully they moved on, so we were lucky, we were all in our office at that time and we were locked in."