Major General Robert Gordon said that by forging a close partnership both sides could overcome what he described as "local problems", according to a statement from the UN Mission in Ethiopia and Eritrea (UNMEE).
Military leaders from both Ethiopia and Eritrea met in Nairobi on Wednesday under the auspices of the Military Coordination Commission (MCC), chaired by the Force Commander.
Under the terms of the peace deal signed by both countries in December 2000, the MCC provides a forum for military leaders to thrash out details surrounding the peace process.
Ethiopia's military team was led by Brigadier-General Yohannes Gebremeskel and Eritrea's military delegation was led by Brigadier-General Abrahaley Kifle.
"I hope that what we have learned over the last six weeks will help us improve and build better mechanisms because this process is about getting the details right and building mutual confidence in our ability to handle local problems," Gordon said.
The statement said he also praised the professionalism of both armies and re-emphasised the importance of the MCC talks where both sides could meet.
Major-General Gordon, who took over as Force Commander in November 2002, said that demining of the routes needed for border demarcation sites was about to begin.
Ethiopia's General Yohannes also emphasised the need to "try to control crises and to try to find solutions", according to the statement.
It added that General Abrahaley said several issues still needed to be resolved, but did not reveal what they were.
The 16th meeting of the MCC is scheduled for 19 March in Djibouti.
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