The extent of damage from the second quake was not immediately clear, though the first caused relatively little damage.
The U.S. Geological Survey said the second quake was centered along the coast below land about 15 miles (24 kilometers) north of the city of Rosa Zarate.
The earlier quake was centered about 21 miles (35 kilometers) from the town of Muisne. It struck shortly before 3 a.m. local time and had a shallow depth of 32 kilometers below the earth's surface.
President Rafael Correa said there was no tsunami alert and called on residents in Quito, where some residents poured into the streets, to return to their homes. The quake was strong enough to trigger a national disaster alert, but Correa deactivated the emergency response a few hours later when local authorities reported the situation was calm.
"These sort of aftershocks are normal but that doesn't mean they're not scary and can cause damage," Correa said in a televised address, adding that aftershocks of this magnitude were normal for up to two months after a major quake like the one Ecuador experienced.
The president said that while some previously ravaged homes suffered more damage, most had already been evacuated and no buildings had collapsed. There were no reports of fatalities, he said.
Security coordination minister Cesar Navas said one person was injured when a wall fell and five others were hurt in panicky efforts to flee buildings.
The magnitude 7.8 earthquake on April 16 was Ecuador's worst natural disaster in decades, killing 661 and leaving more than 28,000 people homeless. It has been followed by hundreds of aftershocks, at least five of them of magnitude 6.0 or higher.
Ecuador was already struggling economically before the April disaster. Correa has hiked taxes to fund the recovery but says it will take years to rebuild the beach towns and tourist hubs leveled by the quake.
Jorge Zambrano, mayor of Manta, one of the areas hit hardest by last month's big quake, said streets were calm.
"It was a big shake and all of us were scared but there are no major problems at the moment," said Zambrano.