The woman tested positive after returning to Abuja from Uganda. Nigerian authorities said Friday they had yet to establish how she contracted the virus.
Air force spokesman Ehimen Ejodame said the aircraft was on a "routine mission" from Benin City in Nigeria's south to the economic hub Lagos when it went down at Igbokoda in Ondo state.
Drinking locally made alcohol is common in Nigeria, Africa's most populous country, especially in rural areas where it is more affordable and poorly regulated.
Details on attacks by armed groups in rural areas are often hard to confirm, and federal government and military authorities have yet to comment on the assault.
The boat was carrying more than 80 people, most of whom were heading to farms for work in Gorau town in the Goronyo local government area of the state, officials said.
