Kenya’s President Uhuru Kenyatta is facing a dilemma in dealing with two key neighbours — South Sudan and Somalia.

After barely a year in office, Kenya’s political leaders are now realising that their country’s economic power cannot always translate into a foreign policy clout.

Kenya and Somalia are at loggerheads over how to govern southern Somalia, currently controlled by Kenyan troops belatedly brought under the aegis of the African Union Mission in Somalia (Amisom).

The Kenyan government has supported an initiative to set up an interim Jubbaland administration whose links with Mogadishu will be tenuous at best.

Diplomatic sources said that Kenya is planning to open consular offices in Jubbaland and Hargeisa in the self-declared independent Somaliland, but Mogadishu is concerned that Nairobi is planting a seed of self-determination for other regions that could cut links with Mogadishu.

The EastAfrican has learnt that the government of President Hassan Sheikh Mohamud, has been particularly upset by the “Usalama Watch” operation in Kenya aimed at kicking out illegal aliens in the country, which has been seen as targeting Somali nationals.

There are also elements within President Mohamud’s government that have never been comfortable with the Kenya Defence Forces’ entry into Somalia in October 2011 and are wary of Kenya’s increased influence in the affairs of Somalia.

However, former Somalia minister Abdirahman Omar Osman, who has just left his job as the spokesperson of the presidency, argued that the Federal Government of Somalia fully supports the KDF military operations in Somalia.

Two weeks ago, a political consul at the Somali embassy in Kenya, Siyad Mohamud Shire, was arrested in a Nairobi suburb during a police swoops under “Usalama Watch,” forcing Mogadishu to recall its ambassador to Kenya, Mohamed Ali Nur, for consultation.

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But despite his “personal challenges” as a leader who faces charges at the International Criminal Court, President Kenyatta seems determined to nudge his country towards a more robust role in regional and African affairs, his engagement with the East (read China) rather than the country’s traditional Western allies being his boldest move so far.

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President Kenyatta didn’t also shy away from kicking up his own diplomatic dust when he spearheaded what is popularly known as the Coalition of the Willing, with Uganda and Rwanda, leaving out Tanzania, which is a member of the East African Community (EAC).

Under President Kenyatta’s watch, the country has not only become more vulnerable to terrorist attacks from Somalia, but the breakdown of law and order in neighbouring South Sudan is also posing serious threats to the country’s interests.

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President Kenyatta, who is also the chairman of the EAC and the Rapporteur of Inter Governmental Authority on Development (Igad), has been working closely with Ethiopia’s Prime Minister Hailemariam Desalegn to mediate in the South Sudan conflict.

Last week in Arusha, President Kenyatta vowed not to allow genocide to take place in South Sudan, where President Salva Kiir and former vice president Riek Machar have plunged their country into a civil war that threatens to tear it apart with serious regional consequences.

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But President Kenyatta’s regional assertiveness is hampered by the historical unreadiness of the country’s army to respond to an out-of-the-blue war next door.

By contrast, last December Uganda swiftly sent troops to South Sudan to strengthen President Kiir’s hand and thus averted a complete takeover by his rival Dr Machar.

Kampala, despite objections from Ethiopia and powerful Western countries, has so far succeeded in tilting the balance of power in Kiir’s favour, and is more influential in South Sudanese affairs than Nairobi.

That is a major blow to Kenya, which had played a lead role in negotiating the deal that led to the birth of South Sudan.

Although Kenya’s parliament recently approved a decision to send hundreds of additional troops to South Sudan, that move has come too late. It is apparent that Kenya has little leverage over South Sudan’s leaders, many of whom have assets in Kenya.

By Malkhadir Muhumed, Fred Oluoch, Rashid Abdi and Trevor Analo