"I regret that I did not talk first" to Minister Jose Angel Cordova, Chen said on the sidelines of a meeting in Cancun about the swine flu pandemic.
Beijing quarantined dozens of Mexicans at the height of the A(H1N1) outbreak, cut flights to Mexico and barred pork imports.
The measures were angrily denounced in Mexico, which was the center of the swine flu outbreak that has since spread around the world, and been declared a pandemic by the World Health Organization (WHO).
In May Mexican authorities had to charter a plane to repatriate 136 of its nationals from China after they were thrown into isolation.
Chen said such measures were not aimed "against the people" but sought to "reduce the number of infections linked to international travel during the first wave of the pandemic and to win time to battle an imminent second wave."
He also thanked Mexican authorities for sharing information about the flu outbreak in a transparent way, "which helped trigger the international reaction."
The A(H1N1) virus has already infected some 77,201 people in 120 countries and led to 332 deaths, according to the latest WHO figures.