They accused officials of the agency of pursuing a driver, leading to the accidental death of two people on Thursday.
The blockade has forced commuters to trek long distances, a source said.
Other people travelling into or out of Onitsha are left stranded.
On Thursday two persons were crushed to death by a truck being pursued by the members of ATMA, while another was seriously injured.
The accident involved a Mercedes trailer, Toyota Hiace bus and a Mitsubishi L300 bus.
An eyewitness said the crash was caused by a speed violation and loss of control by the truck driver.
Confirming the incident, Sector Commander, Federal Road Safety Corps (FRSC), Utten Boyi, said the deceased have been deposited at the morgue.
He warned motorists to desist from excess speed especially in built-up areas, and should use recommended speed limit of 50km/hr.
“Eight persons, comprising five men, one woman and two children, were involved in the crash.
“One male adult sustained serious injury and was rushed to Toronto hospital by FRSC rescue team from Upper Iweka Command, while two other male adults were confirmed dead by the doctor on duty at the same hospital and they have been deposited at the morgue,” he said