The Cranes play Lesotho at home on Saturday, before facing the same side away at the Setsoto Stadium in Maseru.
After a 1-0 away win over Cape Verde in their opening match, Uganda then drew 0-0 with Tanzania in Kampala last month and lead Group L with a two-point gap.
Although impressed by the way the Cranes have been playing recently, Museveni feels there is still room for improvement.
“I have been following you of recent and I thank you for the performance but we need to work harder for better results. I have offered you a chartered plane to Lesotho and UGX 200 million ($52 000) to help you get good results,” Museveni was quoted as saying on the Federation of Uganda Football Associations official website.
Led by captain and Mamelodi Sundowns goalkeeper Dennis Onyango, Uganda are bidding for a second successive qualification for the Afcon finals after participation at the last edition in Gabon.