The sex offence charges against Assange have eventually been dropped but the whistleblower has not left the diplomatic mission, where he was granted asylum, over fears that he might be seized by the UK authorities and extradited to the United States where he is wanted for leaking classified documents.
A source familiar with the matter said the document was initially sealed but unsealed this week for reasons that are unclear at the moment.
On Thursday evening, Seamus Hughes, the deputy director of the Program on Extremism at George Washington University who is known for scrubbing court filings, joked about the apparent error on Twitter, which first brought it to the attention of reporters.
Prosecutors revealed the existence of the sealed indictment inadvertently in a court filing in an unrelated case, WikiLeaks said.
Federal prosecutors in the Eastern District of Virginia have always been investigating Assange, and in the Trump administration had begun taking a second look at whether to charge members of the WikiLeaks organisation for the 2010 leak of diplomatic cables and military documents which the anti-secrecy group published.
But Joshua Stueve, a spokesman for the prosecutors' office that filed the document that was unsealed, admitted the court filing was an "error".
It was not immediately clear what charges Assange would face.
Carlos Poveda, the lawyer of WikiLeaks founder Julian Assange, told Sputnik that Ecuador might extradite his client, suggesting Quito might have reached an agreement for this with London and Washington.
Prosecutors sought to keep the charges confidential until after Assange's arrest, the document shows, saying the move was essential to ensure he did not evade or avoid arrest and extradition in the case.
Later, Dwyer wrote the charges would "need to remain sealed until Assange is arrested".
USA officials have previously acknowledged that federal prosecutors based in Alexandria have been conducting a lengthy criminal investigation into WikiLeaks and its founder.
Since June 2012, Assange has been living in the Ecuadorian embassy in London, afraid that if he steps outside he will be arrested.
"The news that criminal charges have apparently been filed against Mr. Assange is even more troubling than the haphazard manner in which that information has been revealed", Pollack said in an email.
But following a change in the government of the South American nation, Ecuadorean authorities last March began to crack down on his access to outsiders and for a time cut off his internet access.