Assange, 39, an Australian Internet activist believed to be in Britain, denies the accusations and had appealed a lower court order that permitted an international arrest warrant remanding him into custody.
The Svea Appeals Court in Stockholm rejected his appeal Wednesday, saying the allegations merited the arrest warrant issued by the International Criminal Police Organization Interpol Saturday following the district court ruling Nov. 18.
The appeals court acknowledged it reached a different conclusion from the district court "in certain parts" of its ruling, and adjusted the warrant to reflect the crime was "less serious" than originally indicated, but said the "grounds for a remand order remained," Swedish news agency Tidningarnas Telegrambyra reported.
Assange attorney Bjoern Hurtig told the Swedish newspaper Aftonbladet he would appeal the case to the Swedish Supreme Court.
"We are disappointed, but are hopeful about an appeal after the court changed the wording," Hurtig said.
Assange, whose organization published almost a half-million secret documents about U.S. involvement in the wars in Afghanistan and Iraq, is suspected of raping one woman and sexually molesting another during a visit to Sweden to talk about WikiLeaks' publishing of the classified U.S. military documents.
WikiLeaks claimed Monday it was preparing its largest leak ever, about 2.8 million documents, believed to include classified U.S. diplomatic cables revealing corruption allegations against foreign governments and leaders.
One of the leaks indicates Turkey helped al-Qaida in Iraq and the United States supported the separatist Kurdistan Workers' Party in its armed struggle against Turkey for an independent Kurdistan, the London-based pan-Arab newspaper Al-Hayat reported Thursday.
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