A U.S. Customs and Border Protection (CBP) agent (L) stands watch as U.S. troops set up concertina wire at the San Ysidro port of entry during a 'large-scale operational readiness exercise' which briefly closed the border crossing on November 22, 2018 in Tijuana, Mexico.

More than 40,000 immigration court hearings have been canceled since the government shutdown began, straining the country's immigration system.

At the same time, the Pentagon is directing additional funds to militarize the U.S.-Mexico border, extending troop deployment.

The troop extension comes as the partial government shutdown, now the longest shutdown on record, enters its 25th day. President Donald Trump and Congress have been unable to agree on a spending deal to fund the government over the president's demand for $5.7 billion in border wall funding. That has forced the closure of nine federal agencies.

Immigration courts have been frozen since the shutdown began, with all scheduled hearings canceled except for those immigrants in detention centers. According to a report from the Transactional Records Access Clearinghouse at Syracuse University, 42,726 immigration hearings have been canceled as of Jan. 11.

If the shutdown continues through the end of the month, more than 100,000 hearings will be canceled; by March, nearly 200,000 will be canceled.

With a court backlog of over 800,000 pending cases, immigration lawyers expect that canceled hearings will not be rescheduled until at least 2020. Immigrants can remain living in the United States until their court date, a practice colloquially known as "catch and release," which Trump has criticized in the past. As a result of the shutdown, those who would have been deported after their hearing will stay in the country even longer while they await their new court date.

Meanwhile, the Pentagon announced in a statement Monday evening that the troops deployed at the border since last November will remain there through September. Trump ordered the troops to be deployed last fall ahead of the arrival of a migrant caravan traveling from Central America. The troops were originally scheduled to leave on Dec. 15, but the deployment was extended through January before being extended again on Monday.

The Pentagon originally estimated a cost of $72 million to cover the 5,900 troops amassed at the border until Dec. 15, but it is unclear how much the extended deployment will cost. A representative from the Department of Defense told CNBC, "We have not yet determined the force size and composition to meet this request."

The troops will be installing concertina wire on top of existing fencing, as well as using mobile cameras and aviation surveillance.

However, the president has expressed doubts about the effectiveness of parts of the Pentagon's plan. "A drone flying around will not stop [illegal immigration]," he tweeted on Tuesday. "Only a Wall will work."

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