The leader of an armed group that is stopping undocumented migrants who cross into the US from Mexico once boasted about training to assassinate Barack Obama, Hillary Clinton and George Soros, an FBI agent said in court papers on Monday.

Larry Mitchell Hopkins, leader of the United Constitutional Patriots (UCP), whose camouflage-wearing armed members claim to have helped US officials detain some 5,600 migrants in New Mexico’s desert in the last 60 days, was arrested on Friday on a weapons charge.

The UCP claims to have the support of US border patrol at a time when the agency is overwhelmed by record numbers of asylum seeking Central American families.

Dressed in clothing that resembles military fatigues and carrying weapons, members appear in videos disseminated by the group telling migrants, including women and children and in some cases numbering in the hundreds, to stop and wait for immigration agents.

Critics including the American Civil Liberties Union (ACLU) accuse the UCP of being vigilantes who illegally detain and kidnap migrants by impersonating law enforcement.

Hopkins was arrested a day after New Mexico’s Democratic governor, Michelle Lujan Grisham, ordered an investigation of the group, saying in a tweet that “menacing or threatening migrant families and asylum-seekers is absolutely unacceptable and must cease”.

On Monday, Hopkins appeared in court in Las Cruces, New Mexico, to face charges of being a felon in possession of a firearm. The FBI said it found guns during a 2017 visit to his home. Defense attorney Kelly O’Connell said Hopkins planned to plead not guilty and noted that the charges were unrelated to UCP’s actions at the border.

“This is not even dealing with what’s going on right here,” O’Connell said.

UCP spokesman Jim Benvie previously said the group was helping the border patrol and publicizing the “border crisis”. He was not immediately available for comment.

Crowdfunding sites PayPal and GoFundMe last week barred the group, citing policies not to promote hate or violence, after the ACLU called the UCP a “fascist militia”.

In court papers filed on Monday, FBI special agent David Gabriel said in a criminal complaint that in October 2017 the agency received reports a militia was being run out of Hopkins’ home in Flora Vista, New Mexico.

When agents entered the home they collected nine firearms, ranging from pistols to rifles, Horton was illegally in possession of as he had at least one prior felony conviction, according to the complaint.

The FBI said in court papers that in 2006, Hopkins was convicted of criminal impersonation of a police officer and felony possession of a firearm, and that in 1996 he was also convicted on a firearms charge.

Hopkins, the UCP’s national commander, told agents his common-law wife owned the weapons in question, according to court papers. The FBI had received information that the UCP had about 20 members and had AK-47 rifles and other firearms.

“Hopkins also allegedly made the statement that the United Constitutional Patriots were training to assassinate George Soros, Hillary Clinton and Barack Obama” because it believed that they supported leftwing, anti-fascist protesters, the complaint said.

Former state and federal prosecutor David S Weinstein said border patrol’s tacit allowance of the UCP may have let it to go beyond what citizens are legally allowed to do.

“To the extent where the FBI has got involved, I think it’s escalated to a point where they need to send a stronger message out to them that, ‘No, we told you not to do this,’” said Weinstein, a partner at the law firm of Hinshaw and Culbertson.

• This article was amended on 24 April 2019. An earlier version referred to “impersonation of a peace officer”. That should have said “police officer”.