"To address the rock throwers assaulting agents and risking the safety of migrants attempting to cross who were already on the US side, both smoke and minimal countermeasures were deployed", CBP said in a statement.
The Associated Press reported that at least three volleys of gas were launched across the border onto the Mexican side near Tijuana's beach early Tuesday, landing among the migrants, including women and children, as well as press members.
Migrants who spoke with AP said they arrived last month with the caravan from Honduras. After the skirmish, the Border Protection agents detained 25 illegal immigrants while the remainder withdrew back to Mexico after finding a gap in the fence. The agency said small children were also being put over the fence, adding the migrants were "having difficulty accomplishing the task in a safe manner".
An AP photographer at the scene said the migrants began throwing rocks after the tear gas was sacked.
A witness cited by Reuters, said he did not observe any rocks being hurled at the agents, but saw a migrant being hit by an object looking like a gas canister.
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The two parts will be voted on separately on the House floor on Thursday, said Democrats, who will hold a 36-seat majority. The second bill would reopen and fund the Department of Homeland Security (DHS) only on a short-term basis.
Border Protection told AP that its Office of Professional Responsibility will be assessing the incident to see if the amount of force used was justified. At least 100 migrants attempted to enter the United States illegally in the incident, CNN reported.
The incursion took place at a spot where there is border fencing, but it's a very old version that's relatively easy to penetrate. The White House announced in December that Mexico, rather than the USA, will house migrants while they wait for their asylum cases to be processed.
The migrant caravan left Central America in October and travelled 4,300km (2,600 miles) to Tijuana in the hope of reaching the United States and requesting asylum.
"Migrants who participate in these violent events who are fully identified will be deported immediately", the Ministry of Interior said in a statement. The rest asked to be transported back home or dispersed to other parts of Mexico.
In November, after a group of migrants tried to rush the border, McAleenan defended the use of tear gas: "As the events unfolded, quick, decisive and effective action prevented an extremely risky situation".
This latest attempted group-crossing came midway through a partial government shutdown over a dispute between President Donald Trump and Democrats.