"You can't call it a mistake because the prosecutor in question has to make a decision based on the information available at the moment of the decision," Rosander told Al Jazeera on Sunday.
The charges against Assange, which come around a month after Wikileaks incensed the US government by releasing a trove of American military informationabout the war in Afghanistan, quickly spread around the internet.
Assange, whose whereabouts are unknown, denied the allegations on Twitter, saying the chargeswere "without basis and their issue at this moment is deeply disturbing".
Rosander defended her office's conduct, saying the duty prosecutor had followed "normal procedure" and "had to make a decision very quickly".
She said Finne, who withdrew the rape charge on Saturday, "had more information than the prosecutor the previous afternoon".
Finne's office has not contacted Assange and is not searching for him and will make a decision whether to pursue the molestation charge later this week, Rosander said.
After the Swedish tabloid Expressen first published reportsthat the arrest warrant had been issued for Assange, Wikileaks responded on Twitter:"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 caused controversy in Julywhen it released 75,000 classified US military reports containing information about the Nato war effort in Afghanistan.
The US government condemned the release of the documents, saying the website had "blood on its hands" for naming people who had helped its military against groups such as the Taliban and al-Qaeda, and ordered Wikileaks to return the files.
Wikileaks, meanwhile, has said it is plans to reveal more of the remaining 15,000 classified documents it holds, possibly this month or next month.
Two alleged victims
Two women in their twenties made the allegations against Assange, according to Al Jazeera's Paul Brennan, reporting from London.
One woman claimed Assange raped her last weekend in Stockholm, while another alleged he molested her on Tuesday in a separate town in Sweden, Brennan said.
"I think it's quite natural that these rumors happen in a very famous case like this, and I'm not surprised at all," Rosander, the prosecutor's spokeswoman, told Al Jazeera.
She said she could not give any details on the allegations.
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.