Assange's Swedish lawyer said the decision would be appealed to the Supreme Court.
The 43-year-old Australian has been stuck inside Ecuador's London embassy since June 2012 to avoid a British extradition to Sweden, which wants to question him on allegations of sexual assault and rape but have insisted he must come to Sweden first.
Assange's lawyers have argued that the arrest warrant should be repealed because it cannot be enforced while Assange is in the embassy, and Swedish prosecutors had not travelled to London to interrogate him.
"There is no reason to set aside the detention solely because Julian Assange is in an embassy and the detention order cannot be enforced at present for that reason," the Svea Court of Appeal said in a statement.
The court also said Swedish prosecutors had not made enough effort to interrogate Assange outside Sweden and said the "failure of the prosecutors to examine alternative avenues is not in line with their obligation".
Per Samuelson, one of Assange's lawyers, told Reuters he read this to mean that the court believed the defence was right, but that it did not dare take the full consequences and lift the detention order.
"If you don't do it now, the arrest warrant will go next time, that is how it looks, like a warning," he said of the court's comments.
Prosecutor Marianne Ny said in a statement: "Like the court of appeals says, there is every reason to continue considering how the case should be taken forward."
Assange denies the allegations and says he fears Sweden would extradite him to the United States, where he could be put on trial for one of the largest classified information leaks in US history.
Samuelson said Assange would not leave the embassy before he could do so without risking ending up in a US prison.
"This is about the threat of extradition to the US and 35 years of jail there," Assange's lawyer said. "As long as that threat remains, there is no doubt he will stay at the embassy."
Assange was initially taken into custody in London but freed on bail, later claiming political asylum in Ecuador's embassy.
