When an Afghan national on the FBI terrorist watchlist was arrested last Thursday after having spent nearly a year in the U.S., immigration officials said he had been enrolled in a program that tracked his location via ankle monitor, mobile app or telephone.

But the man’s participation in the monitoring program, known as Alternatives to Detention, lasted only a little over two weeks, NBC News has learned. 

Mohammad Kharwin, 48, is believed to have then spent 10 months in the U.S. without any kind of monitoring system, according to sources familiar with his case. 

The national terrorist watchlist indicates Kharwin is a member of Hezb-e-Islami, or HIG, an Afghanistan-based political and paramilitary group that the U.S. has designated a terrorist organization.

HIG was responsible for attacks in Afghanistan that killed at least nine American soldiers and civilians from 2013 to 2015. The group is not seen as a top threat in terms of attacks inside the U.S.

Immigration and Customs Enforcement and Homeland Security Department officials did not immediately respond to requests for comment.

NBC News reported last week that Customs and Border Protection agents first arrested Kharwin on March 10, 2023, near San Ysidro, California, after he crossed the Mexico-U.S. border illegally.

At the time, Customs and Border Protection agents did not have complete information about Kharwin and could not confirm that he was on the terrorist watchlist. So he was treated like other low-threat migrants coming into the U.S.

When border agents released him, Kharwin was referred to Alternatives to Detention, run by Immigration and Customs Enforcement, or ICE. Kharwin was enrolled in the tracking program on March 12, 2023, and then taken out of it on March 28, 2023. It is not clear why he was dropped from the program. 

Roughly a year later, ICE agents arrested Kharwin in February after the FBI passed information to them indicating that Kharwin had potential terrorist ties. But when Kharwin appeared in court, ICE prosecutors did not share some classified information with the immigration judge that purportedly showed Kharwin’s ties to a terrorist group, two U.S. officials said.

Prosecutors argued that Kharwin should be detained without bond because he posed a flight risk, but they did not say he was a national security risk, according to sources familiar with the case. The judge ordered Kharwin released on $12,000 bond.

Several hours after NBC News broke the news last Thursday that Kharwin remained in the U.S., he was arrested in San Antonio and taken into ICE custody, according to a Homeland Security spokesperson.

Experts said Kharwin’s case raises questions about how migrants who may pose a security threat are vetted and tracked inside the U.S. 

It also raises questions about the Alternatives to Detention program, which the Biden administration has vastly expanded as a way to keep tabs on hundreds of thousands of migrants in the U.S. awaiting immigration court proceedings. 

Republicans in Congress, who oppose the program, have cut funding to it, forcing ICE to drop migrants from being monitored, often as soon as they make their first check-ins at ICE offices. 

In February 2023, NBC News reported that Homeland Security officials said they would have to begin cutting migrants from Alternatives to Detention because Congress had not provided adequate funding. 

It is not clear how ICE determines which migrants to drop from the program. The Homeland Security Department can also work with other law enforcement agencies, including the FBI, to gather intelligence and learn the whereabouts of migrants. 

A Homeland Security official told NBC News that many migrants who are determined to be low flight risks are not kept in Alternatives to Detention until their court dates, which could be a year or more into the future. 

An estimated 183,901 migrants have been in Alternatives to Detention for an average of 554 days, according to data provided by Syracuse University’s Transactional Records Access Clearinghouse for immigration data. At the time Kharwin was dropped from the program, 281,613 migrants had been in the program for an average of 429 days.

A source familiar with the program who spoke on condition of anonymity defended it and said Alternatives to Detention is “the only way to track an individual through GPS technology.” The source added, “Otherwise, you’re relying on people to show up on their own accord.”

Alternatives to Detention began in 2004, during the Bush administration. According to the Homeland Security Department, the number of migrants absconding from the program has “dropped dramatically” in recent years, and enrollment in Alternatives to Detention increases the chances that immigrants show up for their immigration court hearings. 

Immigration advocates praise the program as a more humane and less costly way for the government to keep tabs on migrants awaiting hearings. Republicans in Congress have pressed Homeland Security Secretary Alejandro Mayorkas for not filling all beds in ICE detention facilities, instead. 

It is rare for migrants crossing the southern border to be on the terrorist watchlist.

An NBC News analysis found that the percentage of migrants on the terrorist watchlist as a proportion of the total number of Customs and Border Protection encounters across all U.S. borders was slightly lower during the Biden administration than during the Trump administration. It remained an average of 0.02% during the Biden administration, lower than the 0.05% under former President Donald Trump.