Annan spoke in a video shown at a news conference in Yangon, where his commission issued its interim recommendations for long-term solutions to conflict between Muslim Rohingya and Rakhine Buddhists in Rakhine state. The commission was established last year at the behest of Myanmar's leader, Aung San Suu Kyi.
The Rohingya face severe discrimination in Buddhist-majority Myanmar and were the targets of inter-communal violence in 2012 that killed hundreds and drove about 140,000 people - predominantly Rohingya - from their homes to camps for the internally displaced, where most remain.
Annan said there should be an independent and impartial investigation of the attacks on the border guards and subsequent "crimes."
"We strongly believe that perpetrators of these crimes must be held to account," he said.
The commission's call for an investigation falls short of what has been recommended by the UN's special envoy for human rights in Myanmar, Yanghee Lee, who seeks an international inquiry.
The commission was directed to submit recommendations to the government on how it could promote reconciliation, strengthen local institutions, advance development, resolve conflict and provide humanitarian aid in Rakhine state.
"The commission is not mandated to investigate specific alleged human rights violations," the report cautioned. "Rather, it seeks to address institutional and structural issues which undermine the prospects for peace, justice and development in Rakhine, and to propose concrete steps that may contribute to improving the well-being of all communities in the state.
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