The R21 vaccine, developed by researchers at the University of Oxford in the UK, was manufactured by the Serum Institute of India in collaboration with Novavax.
Health Minister Muhammad Ali Pate has stated that these doses mark a crucial step in the country's campaign to eradicate malaria.
Mosquitoes, the primary vectors of the disease, thrive in water and are particularly abundant during the rainy season.
Malaria poses a significant public health threat in Nigeria, impacting approximately 97 percent of the population.
The World Health Organization identifies Nigeria as the country most severely affected by malaria, responsible for 31 percent of global fatalities related to the disease.
The health ministry has announced that the vaccinations, acquired in partnership with the international Vaccine Alliance, Gavi, will be provided at no cost.
A pilot program will commence in two states with the highest malaria prevalence: Kebbi in the north and Bayelsa along the coast, with plans for a nationwide rollout thereafter.
An additional 153,800 doses are anticipated to arrive in the country on October 26, increasing the total number of available vaccines to one million.