The Somali refugee crisis is now a continental problem causing ethnic tension even in the far-flung South Africa, hence presenting states with a tricky choice between hosting refugees and protecting their national interests.
The explosion that killed a man and injured 39 people in Nairobi on June 11 has put back refugees into sharp focus security-wise.
So far, The Kenya Police has interrogated nine suspects most of them Muslims of Somali origin. The most sought suspect, whose photograph was published on the media, Farah Ahmed Hirsi, handed himself to the police. Farah, a Kenyan citizen born in Mandera District in Northern Kenya, is a businessman in Eastleigh, Nairobi, which houses thousands of Somali refugees. He has a Masters Degree in Islamic Studies.
In August 2006 Farah was arrested and questioned about his alleged links to terrorism-and was threatened with deportation to Somalia for allegedly being in Kenya illegally.
This adds to the perception, in certain quarters, of ethnic Somalis in Kenya as a state security risk since the Shifta (bandit) war in the 1960s. This has also presented intractable difficulties to the protection of the increasingly criminalised Somali asylum-seekers and refugees.
Somalia has been ravaged by decades of civil war after the fall of the Siad Barre regime in 1991 sparking off one of Africa's most protracted refugee crises. In the same vein, Somalia-based al-Jihaad fighters alleged to have links with al-Qaeda have the potential to change the security dynamics in the Greater Horn of Africa.
In a post-September 11 (2001) world, refugees are caught in an intricate web of the global "war on terror". Now, they are pawns in a geopolitical game in which they are seen as agents of insecurity and terrorism.
According to the United Nations High Commissioner for Refugees publication 2006 Global Trends, the number of refugees has increased globally since 2002 by 14 per cent to almost 10 million. This is largely as a result of the crisis in Iraq.
In 2006, the main group of refugees under UNHCR's mandate continued to be Afghans (2.1 million), followed by Iraqis (1.5 million), Sudanese (686,000), Somalis (460,000), and refugees from the Democratic Republic of the Congo and Burundi (about 400,000 each).
African governments have become less tolerant and increasingly inhospitable to refugees. Consequently, refugee policies and administrative structures are geared towards keeping refugees and asylum seekers out by closing borders, preventing entry, denying them asylum and sending them back home even forcefully.
With the fall of the Islamic Courts Union in December 2006, thousands of refugees flocked into the common border with Kenya to escape the fighting as the Islamists abandoned Mogadishu and their last strongholds of Jilib and Kismayo in the Juba River Valley to Ethiopian-backed government forces .
Wary of the security repercussions of Islamic militants and their supporters flocking into its soil, Kenya barred over 7,000 Somali refugees from crossing its border with Somalia, precipitating a humanitarian crisis and international outcry.
Meanwhile, the US had entered joined the fight against Islamists, pushing the security imperatives of the 'war on terror' to bear on the Somalia refugee situation.
Over a decade of insecurity in Somalia has forced thousands of refugees to flee the country. The fall of the Siad Barre government pushed over half a million people into Ethiopia and some 200,000 into Kenya. At the height of the civil war between 1991 and 1992, an estimated two million people were internally displaced and 800,000 forced to flee to the neighbouring countries.
The bloody battle for Mogadishu between Ali Mahdi - elected as president by a cabal of Hawiye politicians on 28 January 1991- and General Mahammed Faarah Aideed after 1992, turned Somalia into one of the most unsafe places in the world.
Furthermore, drought, disease, floods and starvation have collectively claimed thousands of lives, displaced some 600,000 people within Somalia and made lives in refugee camps in Kenya unbearable.
A crippling drought between 2005 and 2006 and crop failure in mid-2006, against the backdrop of escalating war, almost wiped out the livelihoods in Southern Somalia and drove many people to refugee camps in north-eastern Kenya as the Islamic Courts Union (ICU) found a firm footing in the country.
The rise of the courts was as dramatic as their fall. In June 2006, the ICU defeated the US-backed warlords' Alliance for the Restoration of Peace and Counter-Terrorism (ARPCT) and took over Mogadishu.
The ICU-ARPCT fighting killed 400 civilians and displaced 1,500, bringing the total of internally displaced persons in Mogadishu to 250,000.
The ICU brought back some order in the war-torn city and much of the South, but its move to impose Sharia on areas under its control forced thousands of people to flee into Kenya.
The fighting between the ICU militants and the Transitional Federal Government (TFG) in Baidoa had 14,000 Somalis crossing the border into Kenya in September 2006. This brought to 34,000 the total of new refugees in 2006, raising the case load of Somali refugee in the country to 190,000.
Despite the ICU's dramatic fall in December 2006, the battles of Baidoa, Bay region, Bandiradley, Mudug, Beledwweyne and Hiran region displaced no less than 25,000 people in central and Southern Somalia.
The emergence of the ICU as a political force invariably brought Somalia into the spotlight of Washington's anti-terrorist strategy in the Horn of Africa. The military-heavy strategies used in the global 'war on terrorism' involved strategies that eventually, worsened the Somali refugee crisis.
The threat of terrorism rather than humanitarian considerations forced America to back Ethiopia to oust the ICU from Mogadishu, paving the way for the Transitional Federal Government (TFG) and Ethiopian troops to take over Mogadishu.
The refugees bore the brunt of security imperatives as Kenya deployed hundreds of soldiers to seal its borders with Somalia. Also, security measures designed to prevent escaping Somali's Islamic fighters and international terrorists from using refugees as cover to enter into Kenya kept thousands of deserving refugee cases on the other side of the border.
Kenyan intelligence sources indicated that al-Sudani, Comorian Fazul Abdullah Mohammed and Kenyan Saleh Ali Saleh Nabhan were among Islamists who fled towards the Kenyan border.
In January 2006, the US launched two air-strikes against suspected al-Qaeda fighters in Somalia -Washington's first overt military intervention in Somalia since 18 of its soldiers were killed in Mogadishu by suspected terrorists in 1993.
During the strikes, the security priorities of crushing Islamic terrorism eclipsed the plight of Somali refugees fleeing the war.
Indeed, the spectre of terrorism has added a new security angle to the challenge of nearly 240,000 Somali refugees in camps in the Horn of Africa.
Although countries like Kenya have adopted democratic systems, Somali refugees are still viewed through a distinct security prism, with the dictates of state security eclipsing the welfare of the refugees.
This is not unique to the Somali refugee situation. While the 1998-2003 civil war in the Democratic Republic of the Congo (DRC) killed some four million people and displaced an estimated 1.1 million Congolese, including 400,000 refugees, the war created new security dynamics involving Rwandese refugees and Congolese citizens of Rwandese stock (the Bunyamlenge).
Rwandese refugees (the Interahamwe Hutu militias who fled to the DRC) accused of perpetrating the 1994 genocide, re-grouped in the refugee camps and started recruiting fighters.
The March to Kinshasa by then Congolese rebel leader Laurent Kabila, Rwanda's Paul Kagame and Uganda's Yoweri Museveni was ostensibly to counter the Hutu militias in the refugee camps exacerbated insecurity.
Similarly, over three million Zimbabwean refugees flocking into South Africa are accused of taking up jobs from poor South Africans and compounding the security situation in the country, making them targets of blistering xenophobia.
Somali refugees in South Africa have also become victims of racial hatred and a violence.
In Diepsloot area in Northern Johannesburg, business rivalry and stiff competition between the locals and refugees has triggered rising tension and violence with locals attacking Somali traders.
Local traders claim that Somali refugees are destroying their livelihoods. "We are under attack from these people," a South African trader was quoted saying. "For example, I have my tuck shop in a certain place - then a Somali places the same business right next to mine. On top of that he sells his goods so cheaply, all my customers end up deserting me! How am I expected to survive?"
The conflict is not unique to Diepsloot. Other areas experiencing the same conflict include KwaNobuhle Township, Plettenberg Bay and Knysna in Eastern Cape Province.
Against this background, the protection of refugees in the background of a "war on terror" requires concerted national, international and regional efforts.
The AU has sent into Somalia a stabilisation force comprising mainly Ugandans, but sporadic violence has prevented the return of refugees.
The East African Community's common refugee registration mechanism, proposed in 2003 should be fast tracked. It may offer a useful framework for responding to Somali refugees by the expanded EAC member states-Kenya, Uganda, Tanzania, Burundi and Rwanda.
On its part, the Inter-Governmental Authority on Development (IGAD) has all along pursued dialogue as the best way to stabilize Somalia. In October 2004, IGAD brokered the peace agreement that led to the formation of the TFG. While dialogue continues to be its best option as a tool for securing a durable solution to the Somali refugee crisis, IGAD must now step up its peace diplomacy.
However, proxy wars involving Ethiopia and Eritrea, and long-running tension between three IGAD's members - Kenya, Ethiopia and Djibouti-and pan-Somali nationalists undermine IGAD's efforts. Ethiopia is backing a military approach to the extremists while Eritrea supports them as part its proxy war against Ethiopia. Kenya maintains a cautious "neutrality."
Lack of resources and weak legal and institutional frameworks have also hindered IGAD's capacity to address insecurity relating to refugees.
The African Union (AU) has viable instruments of addressing the refugee crisis, particularly its 1969 (when it was OAU) Convention Guiding Specific Aspects of Refugee Problems in Africa.
Further, the AU has the 1999 Convention on Combating and Prevention of Terrorism. However, the AU must make clear the definition of terrorism to ensure that the agenda to protect refugees is not eclipsed by the discourse on counter-terrorism.
In this regard, the AU should urge the TFG to open dialogue with broad sections of society to calm growing tensions and prevent new destabilisation, especially by Islamists.
And, as things stand, Somali refugees stand to benefit from a series of international decisions and agendas aimed at seeking durable solutions to the refugee problem. These decisions include the Agenda for Protection (AP), the Convention Plus (CP), the Comprehensive Plan of Action for Somali Refugees (CPA), the UN Joint Needs Assessment and the Somali Reconstruction and Development Programme. More salutary was the formation of the Somali Contact Group in 2006, which has provided a diplomatic vehicle for promoting stability in Somalia.
From a realistic point of view, burden-sharing between Somalia's neighbours and wealthier Western powers is crucial to effective refugee protection and assistance.
Ultimately, the changing image of refugees in the age of terror is likely to continue to undermine protection, putting a heavy responsibility on refugee agencies and civil society to step up the agenda of refugee protection.
Patrick Mutahi is the Director of Eastern and Horn of Africa Programme at Africa Policy Institute (Nairobi)