Relations between Kenya and Uganda have been strained since Museveni seized power, although for much of 1988 and early 1989, Uganda and Kenya vacillated between cooperation and confrontation. In 1987 Kenya's president Daniel arap Moi had accused Museveni of allowing Libya to launch destabilizing attacks on Kenya from bases in Uganda, a charge Museveni steadfastly denied. Kenya nonetheless expelled the Ugandan high commissioner and closed the Libyan People's Bureau in Nairobi, and Uganda retaliated by arresting six Kenyan diplomats, including the acting high commissioner. A flurry of high-level communications succeeded in ending this incident, but each nation's fears of cross-border insurgency were heightened.

The year 1988 had begun on a positive note when the two governments agreed to establish a buffer zone along their common border near Busia. At about the same time, however, the NRM government alarmed Kenyan officials by announcing it was considering shipping imports and exports through Dar es Salaam, Tanzania, rather than Mombasa, Kenya. This would have cost Kenya transit fees and several hundred jobs in its transport industry, and suspicions of economic sabotage began to sour relations between the two countries.

A more serious problem occurred in July 1988, when several Ugandan soldiers attacked fishers at Sumba Island in Kenyan territory on Lake Victoria. Kenyan security forces responded and inflicted several casualties. Charges and countercharges were aired through the rest of 1988. There were also outbreaks of sporadic violence along the border and accusations that Ugandan vehicles were being detained or delayed at the Kenyan border points near Nakuru and Eldoret.

Despite some progress toward peaceful negotiations, the hopeful atmosphere was disturbed on March 2, 1989, when some 300 armed forces, believed to be Ugandans intent on stealing cattle, killed a Kenyan army officer in Kenya's West Pokot District. Kenyan security forces responded, killing seventy-two of the alleged cattle rustlers, by their count. Five days later, the Kenyan government claimed that a military aircraft from Uganda had dropped two bombs near a police post near Oropoi. According to the International Committee of the Red Cross (ICRC), the bombs killed five people and injured seven others. The Ugandan government denied complicity in the attack and suggested that the aircraft had originated in Sudan, a report that appeared to be confirmed by independent observers. Ugandan minister of foreign affairs Tarsis Kabwegyere sought mediation.

In 1990 the acrimony between Uganda and Kenya continued, especially after Ugandan police officials accused President Moi of helping Ugandan dissidents plan to overthrow Museveni. Relations improved after the two leaders met in August and agreed to restore full diplomatic ties and to strengthen border security. However, by year's end, the two countries again were at loggerheads, in part because of Kenyan press allegations that Uganda intended "to establish a Pax Uganda over central and eastern Africa."

Data as of December 1990