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.
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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.
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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