Lt. Gen. Jeffrey Buchanan told the outlet in an interview Monday that the first troops will start heading home in the coming days, since some units have completed the missions they were sent for.
"There is no justifiable reason to flatly deny people the right to apply for asylum, and we can not send them back to danger based on the manner of their entry".
Because of the additional security measures and lane closures, border officials are recommending those who traveling north into the USA prepare to face additional wait times.
Homeland Security officials say some 10,500 migrants are camped along the border and on Monday the country's busiest land border crossing had to be hardened with new razor wire and barriers to try to prevent what authorities feared would be a mass incursion, similar to the violent entrance the migrants into Mexico last month.
Northbound traffic and half the pedestrian crossings at the San Ysidro border point were shut to install new movable wire-topped barriers. The US secretary of homeland security, Kirstjen Nielsen, said that the lanes had been closed temporarily, claiming that Border Patrol officials had been notified that "a large [number] of caravan migrants were planning to rush the border in an attempt to gain illegal access to the US".
Tijuana officials converted a municipal gymnasium and recreational complex into a shelter to keep migrants out of public spaces.More news: Rugby star Jarryd Hayne 'arrested after sex assault claims'
The migrants' expected long stay in Tijuana has raised concerns about the ability of the border city of more than 1.6 million people to handle the influx.
"Most of the caravan are not women and children", an official said, adding that most are men and male teenagers trying to enter the country.
Coronel said he hopes as time passes, many will opt to go home or find jobs in Mexico and integrate into society.
"We are fleeing violence", said Josue Caseres, an entertainer from Santa Barbara, Honduras. "We don't want to cause anybody problems".
The protests came amid what may be a hardening of positions in some northern Mexican states against the migrants.
The move could be announced as soon as Monday evening, officials said.More news: Kemba Walker's 60 Points Not Enough As Jimmy Butler Sinks OT Winner
Unmoved by their plight, many disgruntled Tijuana residents are accusing the migrants of being messy, ungrateful and a danger to their city.
Soldiers work on installing concertina wire at the US-Mexico border.
Trump used Twitter on Sunday to voice support for the mayor.
Trump wrote that like Tijuana, "the U.S.is ill-prepared for this invasion, and will not stand for it".
"Likewise, the United States is ill-prepared for this invasion and will not stand for it, they are causing crime and big problems in Mexico, Go home". It is now Catch and Detain.
Asylum-seekers are encouraged to go to ports of entry to ask for help, but are often forced to wait weeks or months to do so because the US government admits only a limited number at a time for processing.More news: Captain America Easter Egg Spotted in New 'Once Upon a Deadpool' Trailer