ProPublica said the audio features 6-year-old Alison Jimena Valencia Madrid who was separated from her mother last week at a border facility, as well as other children, border patrol agents and consular workers.
The audio was released amid backlash for the Trump administration's "zero tolerance" immigration policy which has led to nearly 2,000 child separations. The administration has fiercely defended their policy which has been criticized by both Republicans and Democrats.
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In the recording, young children can be heard calling out for their parents in Spanish while crying. A border patrol agent can be heard joking by saying, "Well, we have an orchestra here, right?"
A 6-year-old Salvadoran girl can be heard pleading for someone to call her aunt. She said she memorized her aunt's phone number and begins to recite the number to a consular representative.
The audio was given to civil rights attorney Jennifer Harbury by a person who asked not to be identified for fear of retaliation.
President Donald Trump has blamed Democrats as well as criminals trying to enter the country for the policy of separating children from their parents.
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Homeland Security Secretary Kirstjen Nielsen and Attorney General Jeff Sessions have defended the administration's policies saying they are merely enforcing the law.
Nielsen said at a National Sheriffs' Association in New Orleans, "We will not apologize for the job we do, for the job law enforcement does and for the job the American people expect us to do."
U.S. Customs and Border Protection has declined to comment about the audio clip.