He was previously charged last month on one count of conspiring with ex-intelligence analyst Chelsea Manning to gain access to the Pentagon network.
Assange is serving a jail sentence in the UK for breaching bail conditions.
The 47-year-old was found guilty last month after his arrest at the Ecuadorian Embassy, where he had sought refuge since 2012 over sexual assault allegations in Sweden. He denies any wrongdoing.
The new indictment says Assange conspired with Manning in order to obtain and disclose secret US files and also exposed and endangered confidential sources in the Middle East and China.
Wikileaks hit back after the announcement, tweeting: "This is madness. It is the end of national security journalism and the first amendment."
Manning was found guilty in 2013 of charges including espionage for leaking secret military files to Wikileaks, but her sentence was commuted.
She is currently back in jail after refusing to testify.