In succeeding years, supporters of a centralized state vied with those in favor of a loose federation and a strong role for tribally-based local kingdoms. Later in 1964, Obote felt strong enough to address the critical issue of the “lost counties” which the British had postponed until after independence. The combination of patronage offers and the promise of future rewards within the ruling coalition gradually thinned opposition party ranks, as members of parliament crossed the floor to join the government benches. After two years of independence, Obote finally acquired enough votes to give the UPC a majority and free himself of the KY coalition.

The turning point came when several DP members of parliament from Bunyoro agreed to join the government side if Obote would undertake a popular referendum to restore the “lost counties” to Bunyoro. The Kabaka, naturally, opposed the plebiscite. Unable to prevent it, he sent 300 armed Baganda veterans to the area to intimidate the Banyoro voters. In turn, 2,000 veterans from Bunyoro massed on the frontier. Civil war was averted, and the referendum was held. The vote demonstrated an overwhelming desire by residents in the counties annexed to Buganda in 1900 to be restored to their historic Bunyoro allegiance, which was duly enacted by the new UPC majority despite KY opposition. This betrayal led to Buganda`s departure from Obote`s government and they became a strong opposition to his rule.