Representatives from Shimizu Corporation and the ministry held a ceremony in Hanoi on Tuesday.
A ministry official said resolving the issues deriving from Agent Orange is an urgent task for the country, and the project will be highly significant.
The project will begin in November at an airport in the southern city of Bien Hoa. 850,000 tons of soil at this site are believed to be polluted.
Shimizu will use its technology to clean up the soil.
The company says its method is more environmentally friendly and is cheaper than the conventional method of incinerating tainted soil.
More than 3 million people are still suffering from health problems caused by Agent Orange, which the US began using in 1961.
More than 4 decades after the war ended, high concentrations of dioxin are still being detected at nearly 30 locations where the US military stored the agent.
The project is attracting attention because the high cost of removing the pollutant has hampered the efforts to clean up contaminated soil across Vietnam.