At least 13 people, including eight children, have been killed in the strike in el-Obeid city, medics say.
About 85 Ethiopian migrants were trying to leave the country when the accident occurred, authorities say.
In a controversial move, Israel became the first nation to acknowledge Somaliland as an independent state.
The main opposition coalition boycotted the vote after a referendum allowed the removal of term limits.
With tens of thousands of cases waiting to be heard, some people have to wait four years for their trials to start.
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