It will be the second donation from Japan after the first batch of 966,320 doses of AstraZeneca vaccine on June 16.
"The supply is a proof of the country's friendly relationship," the Japanese embassy in Hanoi said in a statement.
Motegi also said arrangements were being made to send one million doses each of AstraZeneca vaccine to Indonesia, Malaysia, the Philippines, Taiwan and Thailand, Reuters reported.
Japan would start to supply 11 million doses to regions including Southeast Asia, Southwest Asia and the Pacific islands through the Covax mechanism from mid-July, he was cited as saying.
Vietnam has received nearly 4.5 million Covid-19 vaccine doses through Covax mechanism, contracts, and donations.
The nation has administered nearly three million doses since early March, fully vaccinated 143,121 people with two doses.