He explained that rock-throwers prevented agents from aiding women and children being passed over concertina wire that had been laid beyond the fence on the US side.
A photographer of the Associated Press (AP) news agency saw at least three volleys of gas launched onto the Mexican side of the border near Tijuana's beach that affected the migrants, including women and children, as well as journalists.
Some of the migrants told the news service they arrived last month with the Honduran caravan.
Customs and Border Protection, the agency that oversees, the Border Patrol, said the tear gas and pepper spray fired this week were aimed away from the women and children along the border line, and directed specifically at the group of rock-throwers. About a third gave up and ran back into Mexico but the remaining 100 threw blankets over the barbed wire that runs along the top of part of the border fence and climb over. 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". "Initial reporting indicates that once the attempted illegal entry was thwarted by agents, the mob began pushing women and minors to the front, forcing minors to climb unsafe concertina wire, and encouraged conveniently invited media to begin filming their illegal acts".
The gases caused people to stop throwing rocks and flee, CBP said.
"Agents deployed smoke, pepper spray and CS gas to a position upwind of the rock throwers and south of the border fence".
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CBP said that under its use of force policy, the incident would be reviewed by its Office of Professional Responsibility.
In a previous incident, US agents launched tear gas across the border after some migrants tried to breach the border following a peaceful march in Tijuana on November 26.
CNN has reached out to Families Belong Together, an advocacy group that works with migrants at the border, but didn't get an immediate response.
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.
This group of migrants thought security at the US-Mexico border would be more relaxed in the early hours of New Year's Day. Others have found jobs in Mexico and tried to settle there.
The Trump administration's use of chemical agents against asylum-seekers comes amid a government shutdown over the president's demand for $5 billion in border wall funding.