The disclosure came after Assistant US Attorney Kellen Dwyer made an unrelated filing on Thursday that contained calls for a judge to keep the filing against Assange sealed.
Prosecutors revealed the existence of the sealed indictment inadvertently in a court filing in an unrelated case, WikiLeaks said.
But British police have said they still intend to arrest Assange if he leaves the embassy because he broke his conditions for bail by taking refuge there.
The revelations comes as Special Counsel Robert Mueller has probed Wikileaks role in publishing emails from the Democratic National Committee and longtime Clinton aide John Podesta. He was detained, according to a court filing, because he "has a substantial interest in terrorist acts" that may be related to convictions against his father-in-law.
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.
USA media were alerted late Thursday to the inadvertent disclosure, thanks to a tweet from Seamus Hughes, deputy director of the Program on Extremism at George Washington University.
Based on the filing, prosecutors may circumvent WikiLeaks and focus on Assange.
Even if he is charged, Assange's coming to the United States to face trial is no sure thing.
When he first sought asylum in the embassy, he was facing possible extradition to Sweden in a sex crimes case. Throughout that time, the US has refused to say whether there are any sealed 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 U.S., where he could face charges over WikiLeaks' publication of classified military and diplomatic documents.