Costing VND270 billion ($10.87 million), including more than VND100 billion from the central budget and the rest from the city's budget, the project will be carried out by the municipal Irrigation Sub-Department in Binh Thuy District.
Work is expected to start in 2023 for completion after two years, said Nguyen Quy Ninh, head of the Irrigation Sub-Department.
Rising 2.6 meters high, the embankment will also prevent deliberate encroachment along the river by residents.
Tra Noc flows into the Hau River, a tributary of the Mekong in Vietnam.
Since 2020, the section to host the embankment has suffered seven instances of erosion that damaged 40 houses.
Can Tho covers 1,140 square kilometers and is home to 1.2 million people.
More than half the city has been suffering from flooding during heavy rains and high tides, with many downtown streets submerged under 0.2-0.6 meters of water.
Rising sea levels caused by climate change, rapid urbanization with too many buildings and infrastructure works built in a short period of time, along with over exploitation of groundwater, are the main factors driving the dilemma.