Ban said the United Nations has repeatedly expressed alarm at reports of "pervasive sexual violence" in camps for the displaced in and around Mogadishu, Nesirky said.
These crimes are underreported because of risks to victims, witnesses and family members as well as stigmatization, he said, and "it takes extraordinary courage for survivors to come forward."
The secretary-general urged the Somali government to ensure "respect for human rights, freedom of expression and fair judicial process," Nesirky said.
The United Nations special representative on sexual violence, Zainab Hawa Bangura, said this month that the Somali government's approach to the case "does not serve the interest of justice; it only serves to criminalize victims and undermine freedom of expression for the press."
Rights groups say the arrests were linked to an increase in media attention given to the high levels of rape and other sexual violence in Somalia, including attacks allegedly committed by security forces.
On January 6, Universal TV, a Somali television station, reported that armed men in police uniform had raped a young woman. The same day Al Jazeera published an article which described rape by security forces in camps for internally displaced people in Mogadishu.
Bekele said the case was a politically motivated attempt to blame and silence those who report on "the pervasive problem of sexual violence by Somali security forces."
The husband, another man and another woman were charged with assisting the alleged rape victim to evade investigation and assisting her to secure a profit for the rape allegation, charges that indicated the government believed there was a conspiracy to discredit it and somehow acquire financial gain, Human Rights Watch said previously.
The Somali capital has moved past the violence that engulfed Mogadishu for much of the last two decades. In a sign of its progress, the United States this month officially recognized the country's government for the first time in two decades. The U.S. hadn't recognized a Somali government since warlords toppled dictator Mohamed Siad Barre in 1991.
Despite the progress, Somali government institutions remain weak and corrupt, and the government relies heavily on the security provided by 17,000 African Union troops in the country.
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