Does federal law require people criminally prosecuted to be in federal jail?

Question

A few months ago, Attorney General Jeff Sessions implemented a "zero tolerance policy", requiring the Department of Justice to criminally prosecute every single person caught crossing the border illegally. This has resulted in large numbers of children being separated from their parents. So today President Trump passed an executive order intended to end the family separation issue. Here is what it says:

The Secretary of Homeland Security (Secretary), shall, to the extent permitted by law and subject to the availability of appropriations, maintain custody of alien families during the pendency of any criminal improper entry or immigration proceedings involving their members.

Now some have argued that this executive order will be overturned because extended detention of children violates the Flores settlement, and the courts may not be willing to modify the Flores settlement. But I'm interested in a different issue.

Under the executive order, parents being criminally prosecuted for crossing the border illegally would be held in detention centers by the Department of Homeland Security as they await trial. My question is, is this permitted under federal law? Or does federal law require that those being criminally prosecuted at the federal level (at least for illegal entry) be held in the custody of U.S. Marshals in federal jail as they await trial?

Here is what this article says:

To be clear, there is no official Trump policy stating that every family entering the US without papers has to be separated. What there is is a policy that all adults caught crossing into the US illegally are supposed to be criminally prosecuted — and when that happens to a parent, separation is inevitable.

Typically, people apprehended crossing into the US are held in immigration detention and sent before an immigration judge to see if they will be deported as unauthorized immigrants.

But migrants who’ve been referred for criminal prosecution get sent to a federal jail and brought before a federal judge a few weeks later to see if they’ll get prison time. That’s where the separation happens — because you can’t be kept with your children in federal jail.

But when the article talks about those referred for criminal prosecution being sent to federal jail, is it just talking about standard practice, or is it talking about what federal law requires?

Answer 1

If someone is arrested by federal agents and referred for indictment, they have to be processed by the federal justice department. Processing includes things like being fingerprinted and going before a judge to get bail set or denied. Federal protocols demand that the prisoner goes through this process without family members.

Once the prisoner is processed, there is no detainment requirement. The prosecutor can request detainment, but prisoners could be released on their own recognizance, on payment of bail, or to another organization. For obvious reasons (flight risk), border crossers are generally released to Homeland Security rather than on their own recognizance or with bail.

According to the LA Times:

Rio Grande Valley border agents have prosecuted 568 adults and separated 1,174 children since zero tolerance began, Padilla said. Of those, 463 were reunited with parents “in a matter of hours” after they returned from court. It wasn’t clear how long the rest were separated.

That was as of June 17th of 2018.

There isn't a breakdown of why some families were separated longer.

TL;DR: No, it is not a requirement that prisoners be kept by the Marshals. It is a requirement that they be processed separately from people not being prosecuted (e.g. their children) and members of the opposite sex (e.g. most spouses). After processing they can return to detainment.

Answer 2

The answer from @Brythan adequately addresses many of the key issues. I'll address another.

It is not uncommon for the federal government to enter into contracts with jails administered by local governments or by private prison operators to detain people who are being incarcerated pending trial on federal criminal charges. Most of the $1.6 billion per year federal pretrial detention budget (as of a 2014 report) is paid to local government jail operators on a contract basis.

Pretrial detention in the federal court system is administered by the Office of Federal Detention Trustee in the Department of Justice who also has a mandate to coordinate with ICE (immigration and customers enforcement) in the Department of Homeland Security, although U.S. Marshals (a different part of the U.S. Department of Justice) are responsible for getting detainees to and from the right places to appear in court when federal criminal defendants are detained prior to trial.

Post-conviction detention administration for people convicted of civilian federal felonies is handled by the Bureau of Prisons (BOP) in the Department of Justice, while people convicted in courts-martial have their detention managed by the Department of Defense. The BOP also does some coordination when attempting to locate people detained on immigration grounds or with the District of Columbia Department of Corrections.