Lauri Love of Stradishall, Suffolk, faces one count each of computer hacking and aggravated identify theft.
If convicted, he could be sentenced to up to 12 years in prison.
They are the latest charges against Mr Love, previously accused of breaching the security of Nasa and FBI, among other US government agencies.
A 2013 US department of energy audit report on Mr Love's activities found personal information on 104,000 people could have been taken.
It estimated the fallout of this to cost the US at least $3.7m (£2.2m), including $1.6m spent on establishing a call centre to deal with people affected by the data breach.
Mr Love is accused of working with at least three other people - who have not been named - to breach the security of the US military, US space agency Nasa, the Environmental Protection Agency and FBI computers.
A campaign has been started to fight any possible extradition bid by the US.