Prosecutors accidentally revealed the sealed indictment in a court filing in an unrelated case in the eastern district of Virginia.
Joshua Stueve, a spokesperson for the attorney's office responsible for the filing, told The Washington Post it had been "made in error" and claimed that Assange was "not the intended name for this filing".
Barry Pollack, one of Assange's attorneys, said, "The only thing more irresponsible than charging a person for publishing truthful information would be to put in a public filing information that clearly was not intended for the public and without any notice to Mr. Assange".
The information was contained in a court filing in an unrelated case. It would also suggest that, after years of internal wrangling within the Justice Department, prosecutors have chose to take a more aggressive tact against the secret-sharing website.
He has long maintained that leaving the embassy would lead to his arrest and attempted extradition to the U.S. The U.S. government has never said if it has sealed charges against Assange, but former President Barack Obama's Justice Department reportedly decided against pursuing charges on the ground that WikiLeaks is too similar to a news organization.
Since June 2012, Assange has been living in the Ecuadorian embassy, afraid that if he steps outside he will be arrested.
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The filing in the Eastern District of Virginia came on August 22, in a case that combines national security and sex trafficking.
However the US Mueller inquiry into alleged Russian election interference has suggested that WikiLeaks was used by Russian intelligence to distribute hacked material.
The defendant in the case, Seitu Sulayman Kokayi, is charged with coercion and enticement of a minor.
When he first sought asylum in the embassy, he was facing possible extradition to Sweden in a sex crimes case.
Legal analysts said the error was likely to have been caused by prosecutors copying and pasting from sealed documents outlining charges against Assange.
The 47-year-old has always denied the allegations, and his supporters claim the accusations were an attempt to possibly extradite him to the United States, where he could face charges over WikiLeaks' publication of classified military and diplomatic documents.