But officials in Ecuador said that by Saturday the number had increased to about 1,100.
"We don't know how long they are going to be here and we expect that more people will be arriving," said Gustavo Samaniego, the mayor of San Lorenzo.
Francisco Ortiz of the Red Fronteriza de Paz, a group representing border communities in Ecuador, said the recent flight was prompted by clashes between Colombia's army and National Liberation Army fighters near their communities.
Ortiz said the refugees arrived on Thursday "in the worst human condition," and that many were scared, hungry and sick.
Lenin Moreno, the Ecuadorean vice president, called on Colombia to resolve the refugee problem.
"It pains us what is happening in our neighbouring country, but unfortunately it is not our problem," Moreno said.
"It is a problem that they should resolve."
Alvaro Uribe, the Colombian president, however, accused his nation's largest guerrilla group, the Revolutionary Armed Forces of Colombia, of forcing peasants to flee to Ecuador in a bid to undermine relations between the nations.
There are currently about 250,000 refugees living in Ecuador, the UN says.
Most of them are Colombians who have fled an internal armed conflict that has raged there for more than 40 years.
The UN estimates that about three million Colombians have been driven from their homes by violence without leaving the country - making it the largest internal refugee population in the world after Sudan.
The government's definition of a refugee puts the number at about two million.