A tornado ripped into a town in northern Mexico, killing at least 13 people and flattening hundreds of homes in a deadly six-second blast of carnage.

The savage twister roared through the Mexican border town of Ciudad Acuna at dawn on Monday, tossing cars and big rig trucks into the air before they smashed into houses and buildings.

Images from the aftermath showed several crumpled vehicles resting against walls and roofs as shellshocked inhabitants of the town of 136,000 struggled to make sense of the devastation.

The tornado came as ferocious weather battered swaths of Mexico and the southern United States, where rescuers hunted for 12 people missing in flash floods across Texas and Oklahoma that left three people dead.

In Mexico, national civil protection coordinator Luis Felipe Puente told Foro TV that "more than 1,000 homes" had been affected.

The tornado swept in at "impressive speed" of 270-300km/h and lasted only six seconds, Puente said.

Coahuila state Interior Secretary Victor Zamora said the death toll rose from 11 to 13. The victims include 10 adults and three children.

Almost 230 people were hurt after getting hit or cut by objects thrown by the wind, Zamora told Milenio television. Of those, 88 were still getting treatment in the afternoon.

Ciudad Acuna Mayor Evaristo Lenin Perez said a seven-year-old boy was missing, while rescuers combed through the rubble to look for any more victims or survivors.

Most of the fatalities were people who were out on the street.

"We have hundreds of houses that are practically destroyed," Perez said, appealing for water, canned food and clothing for the victims.

Authorities opened eight temporary shelters for those left homeless.

The tornado whipped up as heavy rains pounded the city, with hail falling in some areas.