The federal government is so overwhelmed by the current tide of migrants crossing the border it can't provide basic medical screening to all of the children before transporting them - often by air - to longer-term holding facilities across the country, ABC News has learned.

The director of refugee health in the federal Health and Human Services Department "has identified a breakdown of the medical screening processes at the Nogales, Arizona, facility," according to an internal Department of Defense memo reviewed by ABC News. The "breakdown" a systemic failure of the handoff of these children between CBP and HHS.

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Inside the government, officials are sounding alarms, fearing that they and their teams who come in contact with the sick children face potential exposure to infectious diseases from chicken pox to influenza, including rare cases of H1N1, more commonly called swine flu.

Two unaccompanied children were flown from Nogales to California despite having 101-degree fevers and flu-like symptoms, according to the Department of Defense memo. Those children had to be hospitalized.

The memo said pointedly that officials in charge of moving the immigrants from Border Patrol processing centers to Health and Human Services facilities are "putting sick [fevers and coughing] unaccompanied children on airplanes inbound for [Naval Base Ventura County] in addition to the chicken pox and coxsackie virus cases."

The document said three other kids were in the ICU at local hospitals in California, and two of them were diagnosed with strep pneumonia.

Less than a week later, that same Ventura Naval Base suffered an outbreak of pneumonia and influenza among the unaccompanied minors inside the shelter.

"Preliminary reports indicate that several unaccompanied minors in the shelter had become ill with what appears to be pneumonia and influenza," according to a statement from the Administration for Children and Families at Health and Human Services.

HHS told ABC News the children were supposed to be screened for sickness before leaving the Border Patrol screening centers.

"When the children arrive at U.S. border stations," the ACF statement read, "they are screened for health problems and given medical treatment if needed."

But, according to the memo ABC News reviewed, "Curi Kim [the HHS director of the Division of Refugee Health] has identified a breakdown of the medical screening processes at the Nogales, Arizona, facility. The [unaccompanied children] were initially screened and cleared upon entry into that facility with no fever or significant symptoms. They were not however re-screened and cleared for travel and placement at a temporary shelter."

While confirming to ABC News the outbreak occurred, HHS would not respond to inquiries about the DOD memo showing sick children were knowingly sent to Naval Base Ventura prior to the outbreak.

"My biggest concerns are with the health of these children," said Richard Besser, ABC News' chief health and medical editor. "They are victims going through incredibly stressful circumstances and some will have health issues that need to be treated. Some come from countries that don't vaccinate against pneumonia or meningitis. They need those vaccines. Some come from countries where it is flu season. They need that vaccine, too. The big health risks are among these children, not to our communities."

Once kids are in HHS custody they receive exams and vaccinations, and are screened for tuberculosis, according to ACF, but more serious illnesses such as meningitis and polio are of little concern for causing an outbreak.

"Children from this region of the world participate in comprehensive childhood vaccination programs, similar to the United States, and are generally well protected from most vaccine-preventable diseases," ACF said in a statement.

Guatemala, El Salvador and Honduras each have rates of vaccination against preventable illnesses such as polio, tuberculosis, measles and pertussis consistent with the United States, according to the World Health Organization.

Latest data on vaccination rates per country, according to Pan American Health Organization

* In 2010 and 2011, Honduras had rates of 100 percent vaccination for all vaccines listed.

During congressional testimony the first week of July, Texas Gov. Rick Perry said: "We've already had one confirmed case of H1N1 in Texas, and have been informed by our federal partners of two additional cases of type A influenza that are likely to be H1N1, in addition to reports of other illnesses at other detention facilities."

The Texas Department of Health confirmed to ABC News that there have been three flu cases, one confirmed H1N1 and two others being flu type A, or presumptive H1N1.

According to the CDC, between April 12, 2009 and April 10, 2010, the height of swine flu in the U.S., approximately 60.8 million cases occurred, with 12,469 deaths.

The CDC website stated: The H1N1 virus that caused that pandemic is now a regular human flu virus and continues to circulate seasonally worldwide.

(Ross D. Franklin-Pool/Getty Images)