President Rafael Correa said the epicentre was the fishing village of Mompiche on the Pacific coast, about 368km from Quito.
"There are some light injuries because people ran out, or bumped into things," Correa said on state television, adding that there was also some minor damage, mainly to infrastructure already hit by the April disaster.
There was no tsunami warning.
The April 16 earthquake, Ecuador's worst in nearly seven decades, flattened buildings along the coast.
As well as the fatalities, it also injured more than 6000 people, left nearly 29,000 homeless, and caused an estimated US$2 billion (A$2.7 billion) in damage, according to the government's latest tally.
Correa described Wednesday's tremor as another aftershock from the April quake.
"Despite the alarm and the scare and the possibility of new damage ... it's normal, you expect aftershocks for two months after," he said.
-AAP