In a series of tweets Wednesday, the Pennsylvania Democrat accused US Immigration and Customs Enforcement of sending the two back into danger. Before their deportation, the mother and son were held for more a year at a family detention center in Berks County, Pennsylvania.
Casey included an image of a letter he sent to President Donald Trump about the case.
But Homeland Security Secretary John Kelly said there's more to the story.
The mother and son, he said, had exhausted their legal remedies. Their requests to stay in the United States were denied five or six times over the past two years, he said, mostly in proceedings that occurred during the Obama administration.
"You can't pick and choose the laws that you obey," Kelly said Thursday. "And I can't pick and choose the laws that we're by law required to enforce. ... We had a court order to remove her and we did."
Speaking in response to a reporter's question at an event on Central America's future at a Washington think tank, Kelly said members of Congress who have a problem with the country's immigration laws should change them.
"Don't call me or tweet or go to the press with outrageous stories about how we do business," he said.
'We are better than this'
Casey implored the government to find a way to bring the mother and son back.
Gang members are looking for the woman after she witnessed her cousin's murder and then fled Honduras with her son, according to the senator.
"We are better than this, " he wrote in the letter. "You have the power to help this child return to safety."
In the meantime, Casey promised to leverage every federal resource, including the State Department, to keep the mother and son safe in Honduras.
The senator told CNN on Thursday he wasn't convinced by officials' explanations that there was nothing else they could do.
"There's no reason why the administration, Homeland Security, couldn't have come up with a better solution here," Casey said. "So, I'm going to be continuing to follow this case to make sure we do everything we can to protect this mother and her child, even though they've already been deported."
Threatening to deport mothers and children who fled violence isn't the way to keep the United States safe, he said.
"This kind of action undermines the national security. It doesn't help it," he said. "And if they think that we're done asking questions, I'm just getting warmed up."
No more legal options
ICE also said the woman had run out of legal options.
"It's unfortunate that politicians are repeating misleading information and in the process, demonizing the men and women whose job it is to enforce the laws Congress writes," said Liz Johnson, assistant director at ICE.
She said the woman entered the United States unlawfully on December 17, 2015, and was detained the following day.
The case had been denied by the 3rd US Circuit Court of Appeals and Supreme Court, according to Johnson.
ICE officials contacted Casey's office about the case and provided information as it became available, she said.
Attorney: We're hoping they're safe
An attorney for the mother said she's still waiting to hear from her clients, whose sudden deportation Wednesday sent their legal team scrambling.
"We're hoping that she got there safely," attorney Carol Anne Donohoe said.
She declined to name the mother and son out of fear for their security in Honduras.
"The family has already been contacted by persecutors saying they know they are coming back into the country," Donohoe said.
Paperwork the family had filed applying for special immigrant juvenile status
for the son should have stopped the deportation, she said.
It's not fair to claim the family had a chance to make its case in multiple courts, Donohoe said.
"The only thing they reviewed was whether the court had jurisdiction to even hear the case," she said.
Kelly is correct that most of the proceedings occurred during the Obama administration, she said. "But that doesn't mean that this administration can't do the right thing by these families."
'We can't disobey the law'
When he was informed of the deportation, Casey said he called the Department of Homeland Security and ICE and left messages. ICE returned his calls several hours later; Secretary Kelly did not return his calls until early Thursday morning.
"We didn't agree much, but we stated our disagreements," said Casey in a conference call with reporters on Thursday afternoon.
Kelly said he would relay the same message the senator got in a phone call with the head of ICE.
"We can't disobey the law," he said.