"A large amount of data from companies and agencies was taken during the hack, including a large amount of personal data, such as personal identity numbers (personnummer) of people with protected identities," prosecutor Henrik Olin said in a statement.
As the hack also involved attempts to withdraw money from the Nordea bank, the indictment includes charges of aggravated fraud, attempted aggravated fraud, and being an accomplice to attempted aggravated fraud.
"I'd say that Svartholm Warg is the main person and brains behind the hacker attack," Olin told the TT news agency.
However, the prosecutor was uncertain as to why the protected personal data was taken and then spread online.
"We've had a lot of theories but I can't find a motive in the evidence. What I can say is that we're talking about an incredibly technically advanced hack against a large server environment considered to have very high security and that can boost one's status in certain circles," said Olin.
Shortly after the arrest, however, reports emerged that he was wanted in an investigation into a hacker attack against Logica and the Swedish Tax Agency (Skatteverket).
The attacks are believed to have started in 2010 and continued until April, 2012.
According to the indictment, evidence includes a confiscated computer as well as transcripts of online chats between Svartholm Warg and the three other suspects charged in the case.
Since December, Svartholm Warg has been held in a prison in Mariefred in central Sweden where he is serving out a prison sentence related to his activities with The Pirate Bay.
Svartholm Warg and his fellow Pirate Bay co-founders Fredrik Neij and Peter Sunde, as well as financier Carl Lundström, were all convicted in 2009 of facilitating copyright infringement and ordered to pay 46 million kronor ($6.9 million) in damages to the music and movie industry.
While Neij, Sunde, and Lundström all had their 12-month sentences reduced to between four and 10 months on appeal in late 2010, Warg did not attend his appeal hearing and his one-year sentence was upheld.
Prosecutors expect the hacking case to come to trial in late May.