The remaining migrants were taken by bus to the new shelter about 10 miles (15 kilometers) from the border crossing at Otay Mesa and 14 miles (22 kilometers) from San Ysidro, near where people line up to file applications for asylum in the United States.
He has sent troops to the border and issued an order denying the possibility of asylum to migrants crossing the southern border illegally - but that order has since been halted by a USA federal judge. "Stand on my head!" one migrant said, egging his companion on.
Women look through clothes that were donated to the new shelter in an area known as El Barretal on Sunday in Tijuana, Mexico.
The city government of Tijuana announced Saturday that it has closed down a migrant shelter at a sports complex close to the USA border that once held about 6,000 Central Americans who hope to get into the U.S.
US authorities say they can process up to 100 asylum seekers a day.
Some migrants are likely to be economic refugees without a strong asylum claim, but others tell stories of receiving politically motivated death threats in a region troubled by decades of instability and violence.
Officials said all the migrants were being moved to a former concert venue much farther from the border. US officials said agents had been wounded or hit by migrants throwing stones. They turned around and waved to those still on the Mexican side.
Since being transferred to the new shelter, Tijuana's municipal authorities have refused to provide details about the migrants.
Officials said the migrants were not forced to move, but food and medical services at the original camp would no longer be available.
Tijuana Mayor Juan Manuel Gastélum said it is costing the city $25,000 per day to feed and house the 7,000 migrants now in the city.
As of October 1, the IOM has estimated that more than 28,500 people had died.
Melanie Hernandez, a migrant at the new shelter, said the desperate situation created by the rain has "improved the humanitarian response" offered by Mexican and USA non-governmental organizations, many of whom are offering clothes, medical care and some legal services.
But it is still crowded.