Blake Farrey, the 20-month-old who was in custody of child protective services in Michigan, is now in foster care in El Paso, Texas.
"Our primary concern is the safety and welfare of this child. He's seeing a pediatrician and will be receiving any necessary therapy. We also will be seeking appropriate relative placement," said Paul Zimmerman, El Paso Child Protective Services spokesman.
Jenna Farrey, Army Spc. Jeffrey, and their children, Blake and 5-month-old Jackson were reported missing Nov. 15 in El Paso. All but Jackson were found in an Escanaba, Michigan motel on Nov. 17.
A scheduled hearing for Jeffrey, did not take place Dec. 12 because he was indicted the day before.
Jeffrey was indicted on a charge of injury to child by omission, the charge he has been held on at the El Paso County Detention Facility since Nov. 18.
His case has been handed over to Judge Patrick Garcia's 384th District Court. Garcia also is overseeing the case of Jeffrey's wife, Jenna.
Officials have yet to confirm if the body of an infant found in Orogrande, New Mexico is Jackson. The baby's body, believed by investigators to be that of Jackson, was taken to Albuquerque. An autopsy report is pending and could take up to eight weeks.
Jenna is currently being held in El Paso County jail on probation violation charges.
Authorities say she violated her probation by leaving the state, which she could not do under the terms of her probation related to a 2012 guilty plea to child endangerment for leaving Blake home alone last year.
No other charges have been filed at this time against Jenna and there are no hearings currently scheduled for her, according to court records.
Jenna was extradited from Michigan to El Paso on Dec. 3. As she was escorted into the El Paso County jail, reporters asked her what happened to Jackson. Jenna said "no comment."
Jeffrey was extradited back to El Paso by the military on Nov. 18 because he was AWOL.
Jeffrey was in court Dec. 3 on a bond reduction hearing. Magistrate judge James Carter denied the Army specialist's request to have his $1.5 million bond lowered to $50,000.
Attorney Joe Spencer is representing the 22-year-old father. He said a couple of weeks ago that his client was on suicide watch, distraught and very emotional.
During Jeffrey's Dec. 3 hearing, prosecutors also shed more light on the status of Blake. Prosecutor Penny Hamilton said the toddler is "grossly underweight" and was taken by Child Protective Services in Michigan because of significant medical issues.
Prosecutors also said Jeffrey's family is fighting for custody of the boy. His defense attorney told ABC-7 the child neglect did not happen under Jeffrey's watch because he was deployed at that time.