"There are not, nor will there be, foreign military bases in the country," Moreno wrote on Twitter, expressing his commitment to preserving the Galapagos Islands.
Defense Minister Oswaldo Jarrin caused a stir on Monday when he revealed that an air surveillance agreement signed with Washington would allow US planes to refuel or temporarily be stationed at the San Cristobal airport.
Jarrin said those planes would be taking part in surveillance to combat drug trafficking and illegal fishing, but would only use the airstrip "once a month, for no more than three days."
Moreno stressed that "aerial surveillance is a joint activity between several countries to protect this world heritage" site that lies around 1,000 kilometers (600 miles) off Ecuador's Pacific coast.
"Peace, sovereignty and national security are our legacy," added the president.
Jarrin had been called before Congress' international relations commission to explain the US agreement, while several lawmakers voiced concerns over Ecuador's sovereignty and the impact on the environment.
The Galapagos Islands are best known for their unique flora and fauna, which inspired naturalist Charles Darwin to write his landmark 1859 study on evolution, "On the Origin of Species."
They are home to species of tortoises, iguanas, birds and fish found nowhere else.
Ecuador's constitution, adopted in 2008, prohibits the installation of foreign military bases in the country.
Moreno's predecessor, Rafael Correa decided in 2007 not to extend beyond 2009 the lease of a US base in the Manta fishing port, which was used to carry out anti-drug trafficking flights.
However, since last September, US planes started taking off from the southwestern coastal town of Guayaquil on missions to combat drug trafficking and illegal fishing following a new pact signed between Quito and Washington.
Relations between the two countries were tense during socialist Correa's decade in power from 2007-17 but have improved since Moreno took over.
Correa has lived in Belgium since 2017 and sources close to the former president claim he has requested political asylum there.
He is wanted in his homeland on suspicion of kidnapping, a charge he has dismissed as "political persecution."
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