No one had been reported dead or missing, he said.
Dozens of residents climbed onto the roofs or balconies of their homes to protect themselves from the rising waters, according to images released by the Ministry of Defense.
Rain had fallen for 12 hours without interruption, causing six rivers to overflow, Lasso said.
"The priority is to save their lives, let's protect them! We have already rescued 500 people and the work continues," he wrote on Twitter.
Authorities evacuated around 500 people by boat and another 30 by helicopter, the Risk Management Secretariat said.
Around 11,750 people were affected by the floods and 16 lost their homes in the province of Esmeraldas, which borders Colombia.
Classes were suspended in several towns where schools were damaged.
Five health centers were also affected.
Between January and May, 36 people have been killed and more than 99,000 affected across Ecuador.
In March, a landslide caused by heavy rains in the Andean town of Alausi buried dozens of houses, killing around 60 people.
Rescuers are still working to recover the bodies of 13 people who went missing in that disaster.
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