The US government is facing a dilemma over its engagement with the regime in Uganda, whose weak democratic credentials are offset by the fact that it is one of America’s key military allies in the conflict hotspot of Somalia, and the ongoing hunt for the Lord’s Resistance Army (LRA) rebels in Central Africa.

The EastAfrican has learnt that during her visit to the country on August 3, US Secretary of State Hillary Clinton was forced to raise her government’s concerns over President Yoweri Museveni’s prolonged stay in power — which, after 26 years and counting, is marked by deteriorating governance, increasing violations of human rights by state agencies and poor delivery of social services.

These issues, important for the Obama administration, especially during a US election year, had to be raised, alongside the recent upheavals in eastern DR Congo, uncertainties over Kenya’s election in 2013, and the situation in Somalia, where Ugandan and Burundian forces form the major fighting element of the UN funded African Union Mission in Somalia, Amisom.

“Yes, she alluded to Uganda’s internal issues, but her agenda was more about the region as a whole,” said a source who was privy to the discussions, but who preferred anonymity.

However, while Mrs Clinton put in a word about the Ugandan leader’s tenure, the reference to the country’s flagging democratic and human-right credentials had to be made with care, so as not to upset the delicate balance of the US’s geopolitical interests in the region.

This is not the same yardstick that Washington applies to other countries in the region that are seen as lesser military allies.

“Washington’s foreign policy objectives in the region — the war on terror, democracy and economic stability — are sometimes in competition with each other, translating into slightly different approaches in US bilateral relations with Kenya, Uganda, South Sudan, Ethiopia and Rwanda,” said Joel D Barkan, senior associate at the US Centre for Strategic and Internal Studies and professor emeritus of political science at the University of Iowa.

“The US values Uganda’s support for the transitional government in Somalia and its renewed pursuit of the LRA, but is also increasingly concerned about Museveni’s 26-year hold on power,” he added.

Kenya’s case

Kenya, on the other hand — being “the most advanced polity in region”— presents a puzzle of its own, with two prominent politicians in the running for next year’s presidential elections, Uhuru Kenyatta and William Ruto, facing International Criminal Court indictments at The Hague.

Moreover, even in the event that neither Kenyatta nor Ruto win the election, Kenya is still considered a lesser power than Uganda when it comes to regional security and the war on terror.

Until last year, when Kenya joined the fight against Al Shabaab in Somalia, for example, Uganda and Burundi were the only countries contributing troops to Amisom. Next-door neighbour Kenya was nowhere in the picture.

This would explain remarks attributed to Mrs Clinton during her visit in Kenya, to the effect that Kenyatta and Ruto’s candidature was a risk to US relations with Nairobi.

The remarks were made in private meetings with top Kenyan officials, whom Mrs Clinton reportedly told the US would impose sanctions if Mr Ruto or Mr Kenyatta became president.

By contrast, Washington questions Uganda’s democracy and-human rights record only during closed door discussions with the Kampala leadership.

In the wake of last year’s Walk-to-Work protests led by opposition leader Kizza Besigye, for instance, President Museveni has been championing controversial proposals to push through draconian laws targeting opposition politicians in the guise of combating “economic saboteurs.”

The proposed laws would proscribe the right to assemble as well as deny suspects their constitutional right to bail for up to six months.

So, while Mrs Clinton apparently raised concerns about these disturbing trends with the Uganda leadership, while meeting human-rights groups later, she would not come out as categorically as she did in Nairobi over Kenyatta’s and Ruto’s presidential bids.

“I’ve said before, it is critical for all Ugandans — the government and citizens alike — to speak out against discrimination, harassment and intimidation of anyone...You have marshalled the evidence and made the arguments using the rights enshrined in Uganda’s constitution and in international law.

"I want you to know that the US is and will be your partner. I raised these issues with President Museveni today, because this isn’t just about carving out special privileges for any one group; this is about making sure universal rights are protected for all people,” she said while addressing Ugandan human rights activists.

Political analysts see this as Washington’s recognition that Uganda’s disregard for democratic practice means that it is not encumbered by elaborate domestic procedures and restrictions when it comes to deploying troops for critical missions in which the US has an interest.

“The puzzle for Washington is how to achieve both foreign policy objectives rather than choosing one over the other. Put differently, the US wants to have its cake and eat it too. That is the dilemma,” argued Prof Barkan, adding, “My own take is that Washington, and for that matter the rest of the international community, would maximise both its interests and, most important, the interests of the peoples of the region, by not viewing democracy versus counter-terrorism as the choice, because that is a false choice.”

The US Secretary of State and her host also discussed the security situation in the Great Lakes region, particularly the Rwanda-M23-Congo problem, the LRA menace as well as US support in the fight against HIV/Aids.

Even though Ms Clinton’s nine-nation African tour did not include Rwanda, the damage for Kigali had already been done when major donors including the US and the UK cut aid because of the regime’s alleged role in supporting Bosco Ntaganda’s rebels in eastern Congo.

Ms Clinton’s Africa tour, which also saw her visit Nigeria, Senegal, South Africa, South Sudan, Malawi, Benin and Ghana was part of the Obama administration’s new strategy for Africa that focuses on stimulating economic growth, peace and security as well as strengthening democracy.