During the year-long appointment Colonel Howie will help train the Somalia Defence Force and police, a big challenge in a country he described as a "failed state".
Col Howie has extensive military experience and has twice led overseas deployments in the Sinai in 1993 and in Iraq in 2004.
He is a senior officer in the Army's Reserve Forces and has been granted special leave from the Corrections Department for the assignment.
"This is a unique opportunity and I am very much looking forward to what will be a challenging role. Despite some progress, Somalia continues to be a failed state which makes it a particularly difficult UN mission," he said.