A man who was referred for prosecution for illegally entering the U.S. is alleging that he was separated from his daughter after President Trump Donald John TrumpBiden on Trump's refusal to commit to peaceful transfer of power: 'What country are we in?' Romney: 'Unthinkable and unacceptable' to not commit to peaceful transition of power Two Louisville police officers shot amid Breonna Taylor grand jury protests MORE ended his administration's policy of separating families at the border.

The nonprofit Texas Civil Rights Project wrote in a letter to U.S. Customs and Border Protection (CBP) and Immigration and Customs Enforcement on Friday that the man, Mario Perez-Domingo, and his daughter were apprehended by border agents in Texas on or about July 5.

The letters states that Perez-Domingo, who is from Guatemala, told the organization a few days later that “an agent separated his two-year-old daughter from him despite his pleas that she was his daughter, and even having a copy of her birth certificate.”

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The father told the group that he had requested his daughter immediately be returned to him, but that agents said the birth certificate wasn’t authentic.

The organization states in the letter that it was able to verify the birth certificate and that it had confirmed that his daughter was being held by the Department of Health and Human Services's Office of Refugee Resettlement.

“Despite Mr. Perez-Domingo providing the government agent copies of the birth certificates upon apprehension, the agents separated the family without any clear reason provided to our client, in violation of the Executive Order, the injunction in Ms. L., and CBP’s stated policy,” the letter reads, referring to a court order requiring the reunification of all immigrant families separated at the border.

A CBP spokesperson said in a statement to The Hill that Perez-Domingo and a child were arrested on July 5, but that he had said that the child was his niece after initially stating that she was his daughter.

The spokesperson also said that Perez-Domingo said he "had retrieved a fraudulent document from a smuggler in Guatemala in order to support his claim," and that he was trying to bring his niece to her mother in Georgia.

"However, when Border Patrol contacted the child’s supposed mother, the individual had difficulty providing basic biographical information on the child. The child was separated from Mr. Perez-Domingo due to these inconsistencies in his statements as well as admitting to providing a fraudulent document," the spokesperson said.

Trump signed an executive order last month ending his administration’s policy of separating immigrant families captured at the border after facing massive bipartisan backlash over the policy.

The administration is in the process of reunifying the immigrant parents and children separated at the border after a court ordered they be reunited.

The Department of Health and Human Services said in a court filing Friday that it had identified more than 2,500 children between the ages of 5 and 17 who had been separated from their parents.

The department said in a statement that it is not “our objective to reunify all 2,551 minors with the adult whom they arrived here with, because some of those adults are not their parents or pose a clear danger to the children.”

A court has given the administration until July 26 to reunite the separated children with their families.

— This story was updated July 14 at 11:38 a.m.