By Tal Kopan, CNN

(CNN) -- Homeland Security Secretary Kirstjen Nielsen on Tuesday defended an agency policy that will result in more families being separated at the border, saying, under a barrage of questions at a Senate hearing, that similar separations happen in the US "every day."

But Nielsen also agreed with senators that more must be done to protect the children who either come to the US without their parents or are separated from them.

Nielsen was testifying Tuesday at a Senate Homeland Security and Governmental Affairs Committee hearing, where lawmakers on both sides of the aisle raised concerns about what happens to immigrant children who end up in the custody of DHS, who -- by law -- transfers such minors to the custody of Health and Human Services within two days.

"Once you start taking these children, please, I don't think any record should reflect that somehow, you are confident or anybody is confident that they're being placed in a safe and secure environment," said Sen. Claire McCaskill, the top Democrat on the committee.

Nielsen said the department has recently instituted a policy that it will refer everyone caught crossing the border illegally for prosecution, even if they are claiming they deserve asylum or have small children. Any parents who are prosecuted as a result will be separated from their children in the process.

Nielsen said similar things happen in the criminal courts in the US "every day."

"Our policy is if you break the law, we will prosecute you," Nielsen said. "You have an option to go to a port of entry and not illegally cross into our country."

In the past, DHS has used discretion on using the federal courts for families instead of letting the case play out solely in immigration court. Immigration advocates have said migrants may not be savvy enough to understand the ports of entry system, and have raised concerns that asylum seekers are being turned away when they get there, though DHS maintains it follows the law.

The Trump administration last month testified it lost track of 20% -- or nearly 1,500 children -- of the undocumented minors that had been in its custody over a three-month period at the end of 2017.

"We are begging you, if in fact this is going to be the outcome, where we're separating children, in some cases infants, from their parents, we need to know where these kids are," said North Dakota Democrat Heidi Heitkamp. "What you're doing to children when you take them away from their parents is the most trauma impactful thing you can do to a child. So let's be good people and good Americans as it relates to how we treat children."

Nielsen repeatedly agreed that while she plans to pursue the prosecutions policy, she intends to work with HHS to make sure the children are protected.

"I just want to say, I couldn't agree with your concerns more, period," Nielsen said. "We owe more to these children to protect them. So I'm saying I agree, we've taken steps and we will continue to strengthen what our partners do to protect these children."

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