Video shows the agent lifting and slamming the migrant to the ground, then placing a leg on the man's back.
The homeless center said they do not know if the man was undocumented or not, or why he was approached by agents to begin with.
U.S. Customs and Border Protection released a statement.
"Although, at the moment we do not have all the details of what occurred during this incident, CBP takes all allegations of misconduct seriously, investigates thoroughly, and holds employees accountable when policies are violated," the statement said.