USA agents fired tear gas into the crowd, which included children, as a peaceful march turned into chaos.
San Diego Border Patrol Chief Rodney Scott confirmed the report in an interview on Monday, adding the majority of those arrested were adult males.
The agency said that officers chose to use the tear gas "because of the risk to agents' safety".
One White House reporter asked Trump if he was comfortable "gassing children" as he left the White House on Monday to travel to Mississippi.
The refugees are legally allowed to apply for asylum in the U.S., but this process has been known to take as long as a year. The violent clashes took place near the border crossing separating the Mexican city of Tijuana from San Diego.
"Mexico should move the flag waving Migrants, many of whom are stone cold criminals, back to their countries", he said. USA authorities shot tear gas at hundreds of migrants who attempted to storm the U.S. border on Sunday. "Congress, fund the WALL!"
"What's kind of striking to me... is some of the visual and rhetorical parallels between what we're seeing at the border right now and what we often see happen in Israel with the Palestinians". Others continued to approach the border and were repelled by more tear gas.
Image A migrant family runs from tear gas released by US border patrol
The sudden rush overwhelmed Mexican police, who were deployed with large clear shields and full riot gear. A young woman fell to the ground unconscious, and two babies cried, tears streaming from the gas.
The migrants covered their faces to protect themselves from the acrid gas. While cross-border shootings are not common, they do occur.
"We've got to look at the facts here".
US Customs and Border Protection officers "were struck by projectiles thrown by caravan members" and "perpetrators will be prosecuted", US Homeland Security Secretary Kirstjen Nielsen said on Twitter. Now, Trump has responded to the whole ordeal.
"The alarm went off and they began throwing tear gas at us". Many hope to apply for asylum in the USA, but agents at the San Ysidro entry point are processing fewer than 100 asylum petitions a day.
It was not immediately clear whether those throwing objects at U.S. agents were part of the caravan, MSNBC reported. He said CBP does not have rubber bullets in its inventory on the border.
Trump has deployed almost 6,000 troops, on top of more than 2,000 National Guardsmen, but Scott said the Department of Defense was not involved in Sunday's engagement. Most say they are trying to escape poverty and violence in their homelands.
The Washington Post reported on Saturday that the Trump administration had gained the support of Mexico's incoming government for a plan to require asylum seekers to wait in Mexico for their applications to be processed.More news: Thanksgiving parade balloons face possible grounding over wind forecast
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