Sixteen victims were transported to hospitals, and rescue teams are attempting to reach a crane operator, the agency said.
Six ambulances and two EMS command units are responding.
The incident was reported about 10:38 a.m. (11:38 a.m. ET), the ATCEMS tweeted.
The collision came in the Mueller community of northeast Austin. There is a park, children's hospital, apartment complex and shopping center in the area.
CNN's Eliott C. McLaughlin contributed to this report.