Gil Kerlikowske, commissioner of U.S. Customs and Border Protection, said Friday that many of the illegal immigrant children his agents are encountering trying to slip across the U.S.-Mexico border have never even seen a doctor before.

He described scenes of Border Patrol agents changing diapers and heating baby formula in order to care for some of the youngest children, and said agents are being asked to do things way beyond their skill set — particularly for so many of the agents who are young, single men.

“I’ve been down there, a lot, and spent a lot of time and I’ve seen these agents doing incredible things,” he said.

The commissioner was pushing back against a complaint filed by the American Civil Liberties Union and several immigrant-rights groups this week charging that agents and officers have been neglecting or abusing many of the children, verbally or physically.

Mr. Kerlikowske said he’s seen pictures of a birthday cake agents brought in for an 11-year-old who, the commissioner said, had never had a birthday cake before.

The commissioner said the complaint filed by the immigrant-rights groups was “vague” and would take a long time to run to ground.

“I think I’ve pretty much demonstrated my commitment to having complaints investigated, my commitment to making the information as a result of those investigations known,” he said at a forum sponsored by the Center for Strategic and International Studies. “I would tell you in reading a few of the complaints, the lack of specificity, particularly when where, what station, let alone the names of any individual, is extremely troubling.”

He said the vagueness of the complaints means he couldn’t give a time frame on finishing the probe.

But Caitlin W. Sanderson, program director at the Esperanza Immigrant Rights Project, which was one of the groups that filed the complaint, said that sounded like slow-walking the investigation.

“I’m pretty troubled by these comments. He seems to be already setting the groundwork for delaying investigating the mistakes by blaming the children form not remember the names of the officers,” she said.

She said the document they sent contained 116 complaints, listed the names of the children involved, and said they showed a “systematic and systemic” problem with the treatment of the kids.

Ms. Sanderson said even if the individual officers couldn’t be identified, the commanding officers at the facilities could — and she said those where repeated complaints have been lodged should get scrutiny.

All sides agree that the situation is testing the limits of the government’s abilities.

Mr. Koskinen described a number of firsts for some of the children — including the medical checkups.

He said most of the children “have never been treated by a doctor of a clinician until they’ve been encountered by us.”

An internal Border Patrol memo from last month pointed to a number of problems, including the inoculations the children require.

At the time the Defense Department, which was offering some of its facilities to house the children, had insisted the children wait seven days from inoculation before they could enter military bases. That was a problem because U.S. law requires Homeland Security to turn the children over to social workers within three days.

One Border Patrol agent this week told The Times that agents trained to patrol the border were instead doing “babysitting” guard duty.

That agent said some of the more extreme reports included having to separate teenaged boys and girls trying to engage in sex.

“The agents have to keep an eye on them also to make sure no shady happenings happen between the females and the males,” the agent said.

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