Muthaura was among the high-ranking Kenyan officials facing trail at the ICC for violence that followed 2007 elections in Kenya. He faced charges ranging from murder and rape for his role in the post-election violence.
ICC Chief Prosecutor Fatou Bensouda said Monday she was withdrawing the charges because some witnesses were too intimidated to testify, recanted earlier statements or had died. The Kenyan government, she added, hasn't provided her office with important evidence surrounding his case.
"Let me be absolutely clear on one point -- this decision applies only to Mr. Muthaura," she stressed. "It does not apply to any other case."
Muthaura was accused along with Deputy Prime Minister Uhuru Kenyatta, who was declared the winner of recent presidential elections in Kenya. Kenyatta is accused of supporting attacks on supporters of Prime Minister Raila Odinga during the 2007 contest. Odinga lost to Kenyatta in the most recent campaign.
Kenyatta's trial is set for July. He denies that allegations against him and said he saw the case against him collapsing along with Muthaura's.
An estimated 1,000 people died and another 600,000 were displaced in the post-election violence in Kenya. There were few reports of violence following the March 4 contest.