Janet Napolitano, who served as Homeland Security secretary under President Barack Obama, said in an interview Tuesday that she once considered the option of separating families at the border but decided “pretty quickly that it would be a bad idea.”

Napolitano, now president of the University of California system, told the Los Angeles Times that the idea was considered while the Obama administration worked to create a safe area at the border.

“As you work through and you realize the difference between handling these as civil deportation matters as opposed to criminal prosecution matters, it was pretty clear off the bat that this would not be a good idea,” she said. She also said the plan was inconsistent with American values.

“As you work through and you realize the difference between handling these as civil deportation matters as opposed to criminal prosecution matters, it was pretty clear off the bat that this would not be a good idea.” — Janet Napolitano

Nearly 2,300 children have been separated from their families over a six-week period in April and May after U.S. Attorney General Jeff Sessions announced a new “zero-tolerance” policy that refers all cases of illegal entry for criminal prosecution. U.S. protocol prohibits detaining children with their parents because the children are not charged with a crime and the parents are.

The Trump administration has been sending babies and other young children to at least three "tender age" shelters in South Texas, the Associated Press reported late Tuesday.

By law, child migrants traveling alone must be sent to facilities run by the U.S. Department of Health and Human Services within three days of being detained. The agency then is responsible for placing the children in shelters or foster homes until they are united with a relative or sponsor in the community as they await immigration court hearings.

But ]Sessions' announcement last month that the government would criminally prosecute everyone who crosses the U.S.-Mexico border illegally has led to the breakup of migrant families and sent a new group of hundreds of young children into the government's care.

Napolitano said the Obama administration prioritized the “prosecution and deportation of those who committed serious crimes,” such as known gang members.

She said the Trump administration rewrote the priorities and now everyone caught at the border is criminally prosecuted — not just deported. She also told the Times that it was a poor use of funding to tap U.S. attorney’s offices to prosecute what amounts to a misdemeanor for first offenders.

The Obama administration detained families, but Napolitano said the process was stopped after a short time.

Trump is no stranger to political backlash, but the policy of separating children from their parents is starting to divide Republicans.

The signs of splintering of GOP support come after longtime Trump ally, the Rev. Franklin Graham, called the policy “disgraceful.” Several religious groups, including some conservative ones, have pushed to stop the practice of separating immigrant children from their parents.

“Nobody likes” breaking up families and “seeing babies ripped from their mothers’ arms,” presidential counselor Kellyanne Conway said.

Doctors and lawyers who have visited the shelters said the facilities were fine, clean and safe, but the kids -- who have no idea where their parents are -- were hysterical, crying and acting out.

"The shelters aren't the problem, it's taking kids from their parents that's the problem," said South Texas pediatrician Marsha Griffin who has visited many.

The Associated Press contributed to this report.