U.S. Customs and Border Protection says it has released them from custody after holding them for 13 days, which is longer than the 72-hour legal limit.
The agency says the girls are in good health.
Ecuadorian officials say the girls' parents are in New York and have been in touch with their daughters.
Disturbing video released by Customs and Border Protection showed the girls getting dropped from atop a 14-foot-high barrier by smugglers, who then abandoned them in a remote location in New Mexico.
A Border Patrol agent using a remote camera saw it unfold.
Authorities quickly rescued the two sisters, just 3 and 5 years old.
RELATED: Toddler sisters dropped from atop 14-foot wall by smuggler at southern border, disturbing video shows
Smugglers drop toddler sisters from 14-foot border wall, abandon them