Assange, whose whereabouts are unclear, denied the allegations on WikiLeaks' Twitter page."The charges are without basis and their issue at this moment is deeply disturbing."
Assange, an Australian, was in Sweden last week to discuss his work and defend his intent to publish further documents on the war in Afghanistan. He has close contacts in the Nordic country, where WikiLeaks has said it keeps some of its servers.
"We can confirm that he's wanted. He was charged last night — the allegation is suspected rape," said Karin Rosander, Director of Communications at the National Prosecutor's office.
"One is rape and one is molestation," she said, without giving details.
WikiLeaks wrote on Twitter that it has not been contacted by police.
"We were warned to expect "dirty tricks." Now we have the first one," WikiLeaks, whose page has more than 100,000 followers, tweeted.
WikiLeaks was not available by telephone or email when contacted by Reuters.
US officials have called the leak, including more than 70,000 documents detailing the war in Afghanistan, one of the biggest security breaches in US military history.
WikiLeaks promotes the leaking of information to fight government and corporate corruption. Earlier this year, it leaked a classified video showing a 2007 helicopter attack that killed a dozen people in Iraq, including two Reuters journalists.
The Pentagon said this month it would be the "height of irresponsibility" if WikiLeaks went through with a new threat to publish outstanding documents it had on the Afghan war.
It wants the site to expunge all classified material from the Internet and return the material it had to the US government.
