Under a program to control motorbike emissions, it said the city would build 88 inspection centers next year and roll out regulations to test vehicles.
Then, from 2022-23, testing will become mandatory.
The test fee is likely to be VND50,000 ($2.16) but might not be collected from poor people.
Motorbikes that fail to meet emission standards and owned by people living in Districts 1, 3 and 5, considered the city's central area, will be fined, though it is not clear when the fines will begin to be applied.
In 2024 and 2025 another 78 testing centers will be built, and the fines will be extended to districts 10 and Tan Binh.
In 2026 districts 4, 6, 8, 11, Tan Phu, Binh Thanh, Phu Nhuan and Go Vap will also be covered.
The cost of setting up the testing system and hiring staff is estimated at VND553 billion from now until 2023, when the fees and fines will start covering the cost.
Once the system is up and running, the city will be able to cut more than 56,000 tons of carbon monoxide and 4,400 tons of hydrocarbon, both harmful to humans, per year.
In May this year the city's transport department collaborated with the Vietnam Association of Motorcycle Manufacturers (VAMM) to trial the program, checking motorbikes for emissions in the four districts of 1, 3, Phu Nhuan, and Tan Binh.
More than 10,600 motorbikes have been checked, and most of those older than five years failed to meet emission standards.
But Associate Professor Pham Xuan Mai of the HCMC University of Technology said the data from the trial is "not reliable enough" since 10,000 is too small a sample size considering there are almost 10 million motorbikes in the city.
Do Van Chung, deputy head of the Binh Tan District urban management office, said the program would disproportionately burden the poor since most of them drive second-hand motorbikes.
With several million motorbikes in the city, a few hundred inspection centers would be inadequate, he added.
Bui Hoa An, deputy head of the city's transport department, said feedback would continue to be collected for the plan, which "does not aim to reduce just air pollution in the city but also traffic gridlock."
HCMC, Vietnam's largest metropolis with a population of 13 million, has almost nine million registered private vehicles, including 825,000 automobiles and 8.12 million motorbikes, according to the department.