Two of the four allegations against the WikiLeaks founder -- who has been holed up at Ecuador's London embassy since 2012 to avoid extradition -- have reached their statute of limitations after five years.
"Now that the statue of limitations has expired on certain offences, I am obliged to drop part of the investigation," prosecutor Marianne Ny said.
However she said she still wanted to question the 44-year-old Australian over a more serious claim of rape.
The accusations dropped involve one count of sexual assault and another of unlawful coercion. A separate allegation of sexual molestation will run out on August 18.
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Assange has always denied the allegations brought by two Swedish women, and insists the sexual encounters were consensual.
Under Swedish law, if a suspect is not questioned before the deadline expires, they can no longer be tried for the alleged crimes.
Despite repeated attempts, prosecutors have been unable to gain access to Ecuador's embassy.
They initially insisted Assange return to Sweden for interrogation -- a condition he rejected on fears Stockholm could deliver him to US authorities, who may try him for leaking nearly 750,000 classified military and diplomatic documents in 2010.
Attorneys for Assange however say suspicions that Ecuador is using delaying tactics are unfounded.
"The (Swedish) request came in late and is being processed by Ecuador, which will certainly approve it after following its own procedures," Assange's Swedish lawyer Per Samuelsson told AFP earlier this month.