The prosecution's written statement to the court rejected the claim that Assange's lawyer was unaware he was wanted for further questioning.
A representative for the lawyer for the two alleged victims was also present in court.
Kristinn Hrafnsson, a WikiLeaks spokesman, expressed disappointment after the court's verdict.
"I had been moderately hopeful, but this didn't come as a surprise," Hrafnsson said. "Now we will appeal and we hope the higher court will reconsider all the solid arguments we have presented. This has to come to an end."
Assange rocketed to international fame, and infamy, in 2010 after WikiLeaks began helping publish secret government documents online. Ecuador granted Assange asylum in June 2012 and he fled to the country's embassy in London to avoid extradition.