US border staff fired tear gas into Mexico as they tried to stop migrants crossing into California on New Year's Day.
One US border official called the group of around 150 migrants who attempted to breach the fence between the Tijuana side to San Diego "a violent mob".
The US Customs and Border Protection agency said the gas was used to stop people throwing rocks from the Mexican side and not migrants who were trying to cross.
It said "toddler-sized children" were seen being passed over the border fence, with agents unable to assist them because of the rocks being thrown.
Mexican Foreign Ministry spokesman Roberto Velasco said his government regretted "the events" at the border.
He said Mexico advocated "respect for migrants' human rights, security and integrity, while calling for respect for laws on both sides of the border".
Many of the migrants who have gathered at the border in Tijuana were part of the caravan which was making its way through Mexico during the mid-term election campaign.
During the campaign, Donald Trump criticised those in the 7,000-strong caravan as being "very bad people", and described it as an "invasion".
Tijuana has become a flashpoint in the debate over US immigration policy, amid a partial US government shutdown over Mr Trump's demand for $5bn (£3.9bn) in funding for a wall along the border with Mexico.
Reuters reported that US security personnel fired tear gas into Mexico after midnight on New Year's Day as some migrants prepared to climb a border fence.
During a second attempt, migrants began to pass youngsters over razor wire used along the border to the US side.
An AP journalist also saw US agents fire plastic pellets.
US Customs and Border Protection said it responded to the rocks with smoke, pepper spray and tear gas.
It added that 25 migrants were detained while others went back into Mexico through a hole under the fence.
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Customs and Border Protection said the incident would be reviewed by its Office of Professional Responsibility, under its policy on use of force.
Amnesty International described the use of tear gas against migrants "cruel and inhumane" and called for an investigation.