The prosecution does not want to question Assange in London because of the nature of the crimes, and because it would be difficult to get all the necessary evidence if it had to be done via another country's judicial system, Isgren said.
She also rejected his claim that the defense had not been given access to all the relevant evidence against him.
It is "likely" but not certain that Assange would be indicted after questioning, the prosecution told the court. However, the prosecution intends to go forward with the case.
WikiLeaks vows an appeal
The prosecution presented evidence that would constitute probable cause for the case against Assange behind closed doors, in order not to interfere with the investigation.
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.