Border patrol agents apprehend an immigrant who illegally crossed the border from Mexico into the U.S. in the Rio Grande Valley sector, near McAllen, Texas, April 2, 2018.

The prosecution tactic is expected to compound an existing problem: Federal officials are losing track of migrant children in the U.S. foster care system, The Associated Press reported last month. While parents are jailed, children are turned over to the Office of Refugee Resettlement, part of the Department of Health and Human Services. The children are then designated as "unaccompanied minors," AP reported, and the government tries to connect them to family members who are already in the United States.

The new prosecution strategy went into effect this month, the report found, reversing precedent that families would remain together in shelters while undergoing asylum or deportation proceedings. Sessions' policy extends to misdemeanor charges for first-time improper entry, according to the report.

Attorney General Jeff Sessions escalated criminal prosecutions for people crossing the border illegally, including enacting a zero tolerance policy that will see even more parents jailed and separated from their children, NBC News reported this week.

"ORR was unable to determine with certainty the whereabouts of 1,475 [unaccompanied alien children]," Steven Wagner, acting assistant secretary for the HHS' administration for children and families, said at a Senate subcommittee testimony in April. The figure was for 2017.

The ability of HHS to track the well-being of unaccompanied minors is limited by its budget, according to Wagner. U.S. officials have been under scrutiny since 2016, when policies intended to protect children running away from violence in Central America were scaled back, the AP reported.

At the same time federal officials were unable to find children already placed in foster care, Sessions' increasingly strong penalties sent hundreds more into the system, NBC News reported. From October 2017 to mid-April, before the new prosecution strategy officially went into effect, more than 700 children were reportedly separated from their parents at the border, according to NBC News.

While official government figures for May are yet to be released, immigration public defenders told NBC News there has been a large increase in the number of family separations since Sessions' announcement.

Cases such as that of Guatemalan immigrant Esteban Pastor, reported by the Houston Chronicle, are becoming even more frequent. Pastor and his 18-month-old son were jailed after crossing the southern U.S. border last summer, according to the report. Pastor's sick toddler was separated from him and placed in a federal shelter, according to the Houston Chronicle, but he was not told the location.

After three months, Pastor was deported, the report said, with federal agents telling him that his child remained "somewhere in Texas."