(CNN) The toddler pounded her fists on the play mat, sobbing, with no parent to comfort her.

Dr. Colleen Kraft watched from across the room, shaken by what she saw.

"She was just inconsolable. ... We all knew why she was crying," says Kraft, president of the American Academy of Pediatrics. "She was crying because she wanted her mother, and there was nothing we could do."

Kraft had been invited by local pediatricians to visit a government shelter for immigrant children in Combes, Texas. The majority of the kids there, she says, had been separated from their parents.

The heartbreaking scene was unlike anything she'd witnessed in her decades as a pediatrician.

"I've never been in this situation where I've felt so needlessly helpless," she told CNN. "This is something that was inflicted on this child by the government, and really is nothing less than government-sanctioned child abuse."

Kraft visited the shelter -- one of more than 100 in the country -- this spring, shortly before administration officials announced that every person caught illegally crossing the border would be referred for prosecution, effectively making it an official policy to separate children from their parents.

Administration officials have defended the approach, arguing they're protecting children in custody and that separations of immigrant families at the border are no different than what happens when anyone accused of a crime is arrested

But since her visit, Kraft has been trying to convince them otherwise.

The association she leads -- which represents more than 65,000 members across the United States -- has sent multiple letters to the Department of Homeland Security, calling for a change of course.

The pediatricians' group isn't the only one that's taken a stand. So have the American College of Physicians and the American Psychiatric Association . Together, the three organizations represent more than 250,000 doctors in the United States.

"The effect of this type of event will follow these children into adulthood and into their entire lives," Dr. Ana Maria Lopez, president of the American College of Physicians, told reporters Thursday. "Our federal government is causing a situation that is creating a host of potential health consequences for an entire category of people."

Kraft says there's nothing political about the points she and other doctors are making.

"This is injustice against the most vulnerable people on this planet: little children," she says. "And we can't stay silent."

'Toxic stress'

Kraft says separating children from their parents is likely to trigger what's known as a "toxic stress" response

"Toxic stress is prolonged exposure to hormones such as cortisol, epinephrine, norepinephrine -- fight or flight hormones -- and then inflammatory hormones," she says. "In a very young child, that disrupts brain development."

Dr. Colleen Kraft, president of the American Academy of Pediatrics, is pushing for the administration to reverse course on its "zero tolerance" policy.

Possible results include developmental delays, such as problems with motor function or speech. And later in life, she says, kids that experience toxic stress are more likely to have health problems like heart disease, cancer and morbid obesity.

"The younger the child is," she says, "the more likely it is to really do long-term damage and short-term damage."

Children separated from their families at the border aren't the only ones dealing with toxic stress, Kraft says.

Pediatricians across the United States, she says, are sharing growing concerns about their patients as the administration continues its immigration crackdown.

"It's creating a whole generation of kids who are traumatized," she says.

After a separation

In the waiting room of Dr. Julie Linton's office, a 2-year-old boy sat on the floor and refused to let go of his mother's leg.

"It was almost like he wouldn't let her out of his sight," says Linton, a pediatrician in Winston-Salem, North Carolina.

His 5-year-old brother, meanwhile, was sitting quietly in a chair, his eyes glued to the ground.

The two children had been separated from their mother at the border and had just been reunited after three months apart. Linton says the trauma they'd been through was clear.

That was some two years ago, under the Obama administration, when the practice was less common.

Now, Linton says, the situation is far more dire.

"Now it's a systematic policy to create the same kind of trauma that, before, I saw really on a case-by-case basis," she says. "Now we're systematizing something that we know is incredibly harmful and incredibly cruel."

Linton says she sees several trauma-related red flags in immigrant children experiencing toxic stress:

• changes in body function: trouble sleeping, eating or toileting

• changes in behavior: detachment, numbing or anxiety

• changes in development and learning: memory, organization and tantrums that make it impossible to focus on new information

And it's not only happening at the border.

Linton says she's taken care of a number of children who've had a parent deported or taken into custody in front of them.

"Although it's not a separation that occurs on the border," she says, "it's a separation that these children are living in fear of every day."

'Voluminous research'

On a conference call with reporters Thursday, medical experts decried the administration's so-called "zero tolerance" policy.

"Voluminous research shows that parental separation is harmful to children," said Arthur Evans Jr., CEO of the American Psychological Association.

More recently, a Kaiser Family Foundation study found that growing fears in immigrant families are having significant negative effects on children's health.

Deportation fears

It's something pediatricians across the country have noticed among their patients, Kraft says.

"Families are scared. (Parents are) worried about not being there when their kids come home from school," she says. "We have kids that are coming into the office with headaches and stomachaches to keep from going to school, because they're afraid their parents are not going to be there when they get home."

Compounding the problem is immigrant parents' growing distrust of authorities, according to Dr. Marisa Azaret, chief psychologist at Nicklaus Children's Hospital in Miami and a medical contributor for CNN en Español.

"Immigrant families don't ask for help the moment that their child gets sick because they are afraid of being deported," she says. "They don't go to an emergency room because they are afraid. So the impact is long, chronic and toxic."

And growing fear isn't just affecting children in immigrant families, Kraft says. It's also affecting their friends.

"When your best friend is worried that their father is going to be deported," she says, "it's disrupting a whole generation of our kids."