The warrant was issued on Friday evening after two women went to police after having sex with the 39-year-old Australian information activist during his visit to Sweden this week.
"As far as I am concerned there are no longer any grounds to suspect that he committed rape," judicial affairs spokeswoman Eva Finne said.
WikiLeaks shot to prominence in July, after the internet site, which campaigns for freedom of information, published thousands of classified U.S. documents relating to the conduct of the war in Afghanistan.
Assange had rejected the accusations by e-mail, and spoke of "dirty tricks" by those who did not agree with WikiLeaks publishing sensitive documents.
WikiLeaks said in its official blog that it had been made aware of the rape allegations.
"We are deeply concerned about the seriousness of these allegations. We the people behind WikiLeaks think highly of Julian and he has our full support," it said.
The arrest warrant was issued after the two women went to police and said they initially had consensual sex with Assange, which in one case turned into rape and in the other to sexual molestation.
A spokeswoman for prosecutors said the two women had not laid formal charges against Assange, but that given the severity of the accusations and the danger of suppression of evidence, the arrest warrant had been issued.
Assange had while he was in Stockholm agreed to cooperate with the Swedish Pirate Party, which will make Internet server capacity available to the website free of charge.