The prosecutor's office in Stockholm said an arrest warrant was issued for the 39-year-old Australian national late on Friday for suspicion of rape and molestation.
After Swedish tabloid Expressen,first published reports that the arrest warrant had been issued for Assange, Wikileaks responded on Twittersaying: "We were warned to expect 'dirty tricks.' Now we have the first one."
"No one here has been contacted by Swedish police. Needless to say this will prove hugely distracting."
Assange's organisation has caused much controversy recently with the release of 75,000 classified US military documentscontaining information surrounding the wars in Iraq and Afghanistan.
The US government rejected the release of the documents, saying the website had "blood on its hands" for naming people who had helped its military in opposition to groups such as the Taliban and al-Qaeda, and ordered Wikileaks to return the files.
Wikileaks, meanwhile, has said that it is plans to reveal more of the remaining 15,000 classified documents it holds, possibly this month or next month.
Al Jazeera's Paul Brennan, in London, said: "The two alleged victims in this are in their twenties.
"One [alleged insident] is supposed to have happened last weekend in Stockholm and another last Tuesday in Sweden but in a separate town."
Assange was in Sweden last week partly to apply for a publishing certificate to maintain the advantages it receives from the country's whistle-blowing protection laws. Wikileaks also has many of its servers in Sweden.