Storage fungi are among the major factors causing post-harvest deterioration of crop produce worldwide. However, their association to the major factors that contribute to fungal contamination under storage conditions remains under studied in many parts of Sub-Saharan Africa including Ethiopia. Therefore, the current work was carried out with the objectives to identify major factors that contribute to fungal contamination of wheat grains under storage conditions. For this purpose mycological analysis was carried out using 180 wheat grain samples collected from three major wheat growing zones (Arsi, West Arsi and Bale) of South East Ethiopia. Results of the mycological analysis revealed the contamination of wheat grains by fungal species at different locations and storage time with different frequencies. Fungal contamination of samples indicated that highest incidence was observed at West Arsi (96.98%) followed by Bale (91.76%) and Arsi (86.43%). Fungal contamination also varied with storage period with the highest incidence of (98.62%) followed by (89.78%) and (86.77%) was observed after six months, upon harvest and three months of storage, respectively. The highest fungal incidence (98.62%) was recorded after six months storage of wheat grain. Fungal incidence was highly associated with two of the independent variables, namely, temperature and relative humidity of storage in a logistic regression model. However, there is no significant association (p<0.05) with grain moisture content and storage type of wheat grains under storage conditions.