The Netzpolitik website has been suspected of revealing state secrets, resulting in Germany's chief federal prosecutor issuing an investigation of two journalists working at the site.
The case inspired a political row about freedom of speech, with public rallies behind Netzpolitik.
The chief prosecutor's office said it now accepted the justice ministry's evaluation that Netzpolitik did not leak state secrets. However German media said investigations against unnamed state officials were ongoing in conjunction with a suspected breach of confidentiality.
Earlier this year, Netzpolitik reported that Germany's domestic intelligence agency sought more financial support to expand its online surveillance programme. A later article in April examined the spy agency's plans to set up a special unit to monitor social media websites.
Netzpolitik founder Markus Beckedahl and blogger Andre Meister were accused of treason.