The removals of adults and children followed an increased rate of deportation of single adults to Central America since the summer of 2014, the Department of Homeland Security said.
"This should come as no surprise. I have said publicly for months that individuals who constitute enforcement priorities, including families and unaccompanied children, will be removed," Homeland Security Secretary Jeh Johnson said, Reuters reported.
US authorities have cracked down on those living allegedly illegally in the United States in the past year.
The White House would not comment on specifics of the weekend apprehensions by immigration authorities.
"The enforcement priorities laid out by the administration are concentrating our efforts to deport felons, not families, and to prioritise the case of recent border crossers," White House spokesman Josh Earnest said.
The apprehensions targeted adults and children who crossed the southern border illegally after May 1, 2014, the DHS said. They had been ordered removed by an immigration court and exhausted legal remedies and asylum claims, it said.
Most families will be taken to family residential centres before being put on flights to their home countries.
The American Civil Liberties Union (ACLU) condemned the actions and said the deportation policies were rigged against families. "These raids are a scare tactic to deter other families fleeing violence in Central America from coming to the United States," Cecillia Wang, director of the ACLU's immigrants' Rights Project, said in a statement.