(CNN) Following the deaths of two migrant children in US Customs and Border Protection custody, the agency's leader reached out to an influential group of pediatricians for guidance.

Kevin McAleenan, commissioner of US Customs and Border Protection, reached out on Wednesday to Dr. Colleen Kraft, president of the American Academy of Pediatrics. The two spoke on the phone for about 20 minutes.

Kraft, who has previously criticized the agency , described the call as "very positive."

The children's deaths come as more and more families are seeking to cross the border illegally.

As recently as 2013, 90% of migrants attempting to cross the border were adult men. Last month, 59% of apprehended migrants were families or unaccompanied minors, according to Andrew Meehan, CBP's assistant commissioner for public affairs.

"This has created enormous strain on our resources as we tackle the issue of how to deal with large numbers of kids," said Meehan, who confirmed details of the call.

He said it was "critically important" that medical organizations such as the AAP "help inform our policies and procedures."

"We're going to continue to seek the AAP's input as we tackle this crisis," he said.

Kraft said the AAP was eager to help.

"Commissioner McAleenan wanted to communicate to us that CBP recognizes the death of these two children is a major problem and they want to improve the care there and our response was 'let us help you do that,'" she said.

She said she told the CBP commissioner that pediatricians would need "unfettered access" to facilities along the border to assess conditions, offer guidance on protocols and procedures, and care for children.

She said McAleenan told her he would check with his superiors.

"His demeanor was very collaborative," the pediatrician said. "I think their deaths really troubled him, and he wanted us to know they recognize there's a problem."

The pediatricians' group and the CBP have not always had a happy relationship.

In January and then again in March , Kraft wrote to Homeland Security Secretary Kirstjen Nielsen imploring her not to separate children from their parents at the border. Kraft said she did not receive a response.

In June, Kraft told CNN that separating children from their parents at the border "is nothing less than government-sanctioned child abuse."

Earlier this month, following the death of 7-year-old migrant girl Jakelin Caal Maquin , AAP and 12 other medical organizations reached out to Nielsen and McAleenan.

"The death of this young child is tragic and never should have happened," the doctors wrote in a letter Dec. 18. "Many of our organizations have sought to provide expert advice to the federal government, including your agency, about how to best care for and treat immigrant children and pregnant women in your custody. That offer still stands."

According to a statement by the Department of Homeland Security , the initial indication from the hospital that treated Jakelin was that the girl died of "sepsis shock."

Eight-year-old Felipe Gomez Alonzo died on Christmas Eve, less than three weeks after Jakelin died. An autopsy found he had the flu, though an official cause of death has not been determined.

Both children seemed healthy and then within hours became critically ill.

Kraft said that's a message she'd like to get to medical staff along the border: Children, much more so than adults, can look healthy but actually be very sick.

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"A child can be running around and playing while their little systems are breaking down," she said.

Kraft said she hopes her group will get a chance to help the government understand the particular health needs of children.

"When they triage these children and they don't have that pediatric oversight and expertise, they're going to miss kids who don't look like they're ill when they really are," she said.

She added that she hopes to hear back from the Customs and Border Protection commissioner soon.

"The conversation on Wednesday was a first step. A lot more has to happen afterwards," she said.