The latest quake caused no damage or casualties, but shook the ground forcefully in the middle of the night, sending terrified residents running into the street in the devastated resort town of Pedernales.
Some families opted to spend the rest of the night outdoors for fear their homes could collapse like hundreds of buildings did in Saturday's 7.8-magnitude quake, said AFP reporters.
The toll from that quake continued to rise as emergency workers untangled the masses of rubble, often by hand or with basic tools.
President Rafael Correa said officials had now registered 525 people killed, 5,733 injured and 163 missing.
"The death toll will continue to rise, unfortunately, but at a slower pace. Many bodies have already been recovered," he said.
At least 11 foreigners were killed in Saturday's quake, which struck a Pacific coast region popular with tourists. They included citizens of Britain, Canada, Ireland and several Latin American countries.
Ecuadoran authorities called the latest quake an aftershock -- one of more than 500 since Saturday, they said.
The US Geological Survey said it struck at 3:33 am (0833 GMT) at a depth of 16 kilometers (10 miles).
Saturday's quake is the worst to hit Latin America and the Caribbean since the 2010 earthquake in Haiti, which killed between 200,000 and 250,000 people.
Rescue teams worked through the night in the wreckage of coastal towns such as Pedernales and Manta, where the stench of rotting bodies has been growing stronger in the tropical heat.
Hope of finding more victims alive was fading fast.
One of the bodies pulled from the ruins was that of six-year-old Jose David Eras, a Colombian-Ecuadoran boy trapped beneath the rubble of a hotel in Pedernales -- one of around 800 structures toppled in the quake.
Both countries had been on tenterhooks awaiting news of his fate after rescue workers detected signs of life in the debris using a special scanner.
But the Colombian foreign ministry said his lifeless body had been found.
Pope Francis sent Ecuadorans a message of solidarity, his second since Saturday's quake.
"I want to express our closeness and our prayers to our Ecuadoran brothers," he said during his general audience on Saint Peter's Square at the Vatican.
Relatives of the missing have voiced frustration with the pace of the rescue operation.
"Ecuador is not prepared for such a catastrophe," said 27-year-old Samantha Herrera, who was searching for her missing brother Tuesday near a ruined hotel.
Correa handed out food and water in the disaster zone Tuesday, saying he was "exhausted" but vowing to get aid and supplies to victims and rescue workers.
"It is very hard, but we are moving forward," he told AFP in Manta, which resembled a war zone.
Many businesses up and down the coast have closed their shutters, fearing looters -- which has made it all the more difficult to find food and basic necessities.
Fears rose for thousands of people left homeless, prey to disease-bearing mosquitoes and dirty drinking water.
Hundreds of emergency workers from Colombia, Mexico, El Salvador, Spain and other countries were helping overwhelmed Ecuadoran officials.
In Pedernales, a football stadium was serving as a makeshift morgue, as well as a medical and distribution center.
But not everyone was able to get help.
"We came here to ask for food but they've already handed out the supplies," Gema Guillen, a mother of three, told AFP.
The family lost their home in the quake and was now sleeping on the ground, she said.
"There are no tents for people who have been left with no roof over their heads. We need them," said Joffre Gordon, an air force officer leading emergency operations at a base in Manta.
The Inter-American Development Bank announced it would extend Ecuador an emergency loan of up to $300 million.
Correa said rebuilding would cost up to $3 billion and could take two or three years.