Tanzania was expected to send five athletes to the championships in Asaba but officials said they were dissatisfied with the travel arrangements to the event as well as the threat from extremist groups in the region.
The prelude to the games has been marred by scenes of athletes stranded at Lagos airport who have been unable to take connecting flights to Asaba.
Wilhelm Gidabuday, secretary of Athletics Tanzania, said: "The organisers of the African championship acted too late in sending the invitation letters, and they also failed to assure us that we would get visas on arrival in Nigeria.
"We are also concerned about the safety since the Niger Delta region where the event is being held has been put on security alert due to danger of attacks by the Boko Haram extremist groups."
Francine Niyonsaba, Burundi's Olympic 800m silver medalist, shared pictures of herself, and other teammates camped on the airport floor, resting on their luggage on social media.
"Bad situation in Nigeria before African championship in ASABA 2018," she tweeted.
Events at the championships have been rescheduled after more than 300 athletes from 20 countries were delayed in Lagos and unable to be at the track for the 1 August start.